diff --git a/precommit/src/main/shell/core.d/patchfiles.sh b/precommit/src/main/shell/core.d/patchfiles.sh
index 67dec857a..d8dd4d5db 100755
--- a/precommit/src/main/shell/core.d/patchfiles.sh
+++ b/precommit/src/main/shell/core.d/patchfiles.sh
@@ -346,15 +346,18 @@ function patchfile_dryrun_driver
 ## @stability    evolving
 function dryrun_both_files
 {
-  # always prefer the patch file since git format patch files support a lot more
-  if [[ -f "${INPUT_PATCH_FILE}" ]] && patchfile_dryrun_driver "${INPUT_PATCH_FILE}"; then
-    INPUT_APPLY_TYPE="patch"
-    INPUT_APPLIED_FILE="${INPUT_PATCH_FILE}"
-    return 0
-  elif [[ -f "${INPUT_DIFF_FILE}" ]] && patchfile_dryrun_driver "${INPUT_DIFF_FILE}"; then
+  # prefer the cumulative diff: it represents the PR's net change and avoids
+  # stale-file bugs when per-commit .patch stanzas add then rename/delete files
+  # (YETUS-983). Binary files are preserved when the diff is generated locally
+  # with --binary.
+  if [[ -f "${INPUT_DIFF_FILE}" ]] && patchfile_dryrun_driver "${INPUT_DIFF_FILE}"; then
     INPUT_APPLY_TYPE="diff"
     INPUT_APPLIED_FILE="${INPUT_DIFF_FILE}"
     return 0
+  elif [[ -f "${INPUT_PATCH_FILE}" ]] && patchfile_dryrun_driver "${INPUT_PATCH_FILE}"; then
+    INPUT_APPLY_TYPE="patch"
+    INPUT_APPLIED_FILE="${INPUT_PATCH_FILE}"
+    return 0
   else
     return 1
   fi
diff --git a/precommit/src/main/shell/plugins.d/github.sh b/precommit/src/main/shell/plugins.d/github.sh
index ede2f0ce5..c5613cec0 100755
--- a/precommit/src/main/shell/plugins.d/github.sh
+++ b/precommit/src/main/shell/plugins.d/github.sh
@@ -346,6 +346,7 @@ function github_determine_branch
 ## @param        PR number
 ## @param        patch output file
 ## @param        diff output file
+## @param        skip_patch (optional, default false) - skip format-patch generation
 ## @return       0 on success
 ## @return       1 on failure
 function github_generate_local_diff
@@ -353,6 +354,7 @@ function github_generate_local_diff
   declare input=$1
   declare patchout=$2
   declare diffout=$3
+  declare skip_patch=$4
   declare base_ref
   declare base_sha
   declare head_sha
@@ -415,16 +417,18 @@ function github_generate_local_diff
     return 1
   fi
 
-  echo "  Generating patch/diff locally via git"
-
-  if ! "${GIT}" format-patch --stdout "${merge_base}..${head_sha}" > "${patchout}" 2>/dev/null; then
-    yetus_debug "github: git format-patch failed"
-    popd >/dev/null || true
-    return 1
+  if [[ "${skip_patch}" != true ]]; then
+    echo "  Generating local patch via git format-patch"
+    if ! "${GIT}" format-patch --stdout "${merge_base}..${head_sha}" > "${patchout}" 2>/dev/null; then
+      yetus_debug "github: git format-patch failed"
+      popd >/dev/null || true
+      return 1
+    fi
   fi
 
-  if ! "${GIT}" diff "${merge_base}..${head_sha}" > "${diffout}" 2>/dev/null; then
-    yetus_debug "github: git diff failed"
+  echo "  Generating local binary diff via git diff --binary"
+  if ! "${GIT}" diff --binary "${merge_base}..${head_sha}" > "${diffout}" 2>/dev/null; then
+    yetus_debug "github: git diff --binary failed"
     popd >/dev/null || true
     return 1
   fi
@@ -480,10 +484,8 @@ function github_locate_pr_patch
     return 1
   fi
 
-  # we always pull both the .patch and .diff versions
-  # but set the default to be .patch so that binary files work.
-  # The downside of this is that the patch files are
-  # significantly larger and therefore take longer to process
+  # We pull both .patch and .diff versions. The diff is preferred
+  # (see dryrun_both_files / YETUS-983); .patch is kept as a fallback.
 
   apiurl="${GITHUB_API_URL}/repos/${GITHUB_REPO}/pulls/${input}"
 
@@ -515,7 +517,7 @@ function github_locate_pr_patch
           "${GITHUB_AUTH[@]}" \
          "${GITHUB_API_URL}/repos/${GITHUB_REPO}/pulls/${input}"; then
     yetus_debug "github_locate_patch: API patch download failed"
-    if ! github_generate_local_diff "${input}" "${patchout}" "${diffout}"; then
+    if ! github_generate_local_diff "${input}" "${patchout}" "${diffout}" false; then
       yetus_debug "github_locate_patch: local git fallback also failed"
       return 1
     fi
@@ -523,15 +525,17 @@ function github_locate_pr_patch
   fi
 
   if [[ "${diffgenerated}" != true ]]; then
-    echo "  Diff data at $(date)"
-    if ! "${CURL}" --silent --fail \
-            -H "Accept: application/vnd.github.v3.diff" \
-            --output "${diffout}" \
-            --location \
-            "${GITHUB_AUTH[@]}" \
-           "${apiurl}"; then
-      yetus_debug "github_locate_patch: cannot download diff"
-      return 1
+    if ! github_generate_local_diff "${input}" "${patchout}" "${diffout}" true; then
+      echo "  Local binary diff failed, falling back to API diff at $(date)"
+      if ! "${CURL}" --silent --fail \
+              -H "Accept: application/vnd.github.v3.diff" \
+              --output "${diffout}" \
+              --location \
+              "${GITHUB_AUTH[@]}" \
+             "${apiurl}"; then
+        yetus_debug "github_locate_patch: cannot download diff"
+        return 1
+      fi
     fi
   fi
 
diff --git a/precommit/src/main/shell/test-patch.sh b/precommit/src/main/shell/test-patch.sh
index 518afd8c2..b471ccf91 100755
--- a/precommit/src/main/shell/test-patch.sh
+++ b/precommit/src/main/shell/test-patch.sh
@@ -1441,10 +1441,7 @@ function apply_patch_file
 {
 
   if [[ "${INPUT_APPLIED_FILE}" ==  "${INPUT_DIFF_FILE}" ]]; then
-    add_vote_table_v2 '-0' patch "" "Used diff version of patch file. Binary files and potentially other changes not applied. Please rebase and squash commits if necessary."
-    if [[ "${GITHUB_ACTIONS}" == true ]]; then
-      echo "::warning::Used diff version. Binary files and potentially other changes not applied. Try a rebase and/or squashing commits."
-    fi
+    add_vote_table_v2 0 patch "" "Used cumulative diff to apply patch. Per-commit history not preserved."
     big_console_header "Applying diff to ${PATCH_BRANCH}"
   else
     big_console_header "Applying patch to ${PATCH_BRANCH}"
diff --git a/precommit/src/test/shell/git_binary_diff.bats b/precommit/src/test/shell/git_binary_diff.bats
new file mode 100644
index 000000000..1c233de87
--- /dev/null
+++ b/precommit/src/test/shell/git_binary_diff.bats
@@ -0,0 +1,118 @@
+#!/usr/bin/env bash
+# Licensed to the Apache Software Foundation (ASF) under one or more
+# contributor license agreements.  See the NOTICE file distributed with
+# this work for additional information regarding copyright ownership.
+# The ASF licenses this file to You under the Apache License, Version 2.0
+# (the "License"); you may not use this file except in compliance with
+# the License.  You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+load functions_test_helper
+
+TESTREPOS=()
+
+init_test_repo() {
+  local repodir
+  repodir=$(mktemp -d /tmp/yetus-bats-XXXXXX)
+  TESTREPOS+=("${repodir}")
+  unset GIT_DIR GIT_WORK_TREE GIT_DISCOVERY_ACROSS_FILESYSTEM
+  export GIT_CEILING_DIRECTORIES=/tmp
+  pushd "${repodir}" >/dev/null || return 1
+  git init -q --initial-branch=main
+  git config user.email "test@test.com"
+  git config user.name "Test"
+  git config commit.gpgsign false
+  git config tag.gpgsign false
+  git config core.hooksPath /dev/null
+}
+
+teardown() {
+  popd >/dev/null 2>&1 || true
+  for d in "${TESTREPOS[@]}"; do
+    rm -rf "${d}"
+  done
+  TESTREPOS=()
+  if [[ -n "${TMP}" ]]; then
+    rm -rf "${TMP}"
+  fi
+}
+
+@test "git diff --binary round-trip preserves binary content" {
+  init_test_repo
+
+  echo "initial" > readme.txt
+  git add readme.txt
+  git commit -q -m "initial"
+
+  git checkout -q -b feature
+  printf '\x00\x01\x02\x03BINARY\xff\xfe' > binary.dat
+  echo "modified" > readme.txt
+  git add binary.dat readme.txt
+  git commit -q -m "add binary"
+
+  local merge_base
+  merge_base=$(git merge-base main feature)
+  git diff --binary "${merge_base}..feature" > "${TESTREPOS[0]}/test.diff"
+
+  git checkout -q main
+  git apply --binary "${TESTREPOS[0]}/test.diff"
+
+  [ -f binary.dat ]
+  local actual
+  actual=$(od -A n -t x1 binary.dat | tr -d ' \n')
+  [ "${actual}" = "0001020342494e415259fffe" ] # pragma: allowlist secret
+  [ "$(cat readme.txt)" = "modified" ]
+}
+
+@test "YETUS-983: format-patch leaves stale file after add-delete, cumulative diff does not" {
+  init_test_repo
+
+  echo "initial" > Helper.java
+  git add -A && git commit -q -m "initial"
+
+  git checkout -q -b feature
+
+  printf 'public class BigController {\n    public void doStuff() {}\n}\n' > BigController.java
+  git add BigController.java && git commit -q -m "add BigController"
+
+  printf 'public class BigController {\n    public void doStuff() {}\n    public void doMore() {}\n}\n' > BigController.java
+  git add -A && git commit -q -m "modify BigController"
+
+  git rm -q BigController.java
+  printf 'public class SmallController {\n    public void doStuff() {}\n}\n' > SmallController.java
+  git add -A && git commit -q -m "replace BigController with SmallController"
+
+  printf 'public class SmallController {\n    public void doStuff() {}\n    public void doExtra() {}\n}\n' > SmallController.java
+  git add -A && git commit -q -m "modify SmallController"
+
+  local merge_base patchfile difffile tmpfiles
+  merge_base=$(git merge-base main feature)
+  tmpfiles=$(mktemp -d /tmp/yetus-bats-XXXXXX)
+  TESTREPOS+=("${tmpfiles}")
+  patchfile="${tmpfiles}/multi.patch"
+  difffile="${tmpfiles}/cumulative.diff"
+  git format-patch --stdout "${merge_base}..feature" > "${patchfile}"
+  git diff --binary "${merge_base}..feature" > "${difffile}"
+
+  # format-patch dry-run passes (this is the YETUS-983 trap)
+  git checkout -q main
+  git apply --binary --check -p1 "${patchfile}"
+
+  # format-patch actual apply "succeeds" but leaves stale file
+  git apply --binary -p1 "${patchfile}"
+  [ -f BigController.java ]
+
+  # cumulative diff produces correct tree
+  git checkout -f -q main
+  git clean -fd -q
+  git apply --binary -p1 "${difffile}"
+  [ ! -f BigController.java ]
+  [ -f SmallController.java ]
+}