diff --git a/scripts/generate-diff.sh b/scripts/generate-diff.sh
index 21bd781..bcec030 100644
--- a/scripts/generate-diff.sh
+++ b/scripts/generate-diff.sh
@@ -6,9 +6,17 @@ set -euo pipefail
 git fetch origin main --depth=100
 
 if [ -n "${PREV_SHA:-}" ] && git cat-file -e "${PREV_SHA}^{commit}" 2>/dev/null; then
-  echo "Generating incremental diff from ${PREV_SHA} to HEAD"
-  git diff "${PREV_SHA}...HEAD" > pr.diff
-  echo "incremental=true" >> "$GITHUB_OUTPUT"
+  OLD_BASE=$(git merge-base origin/main "$PREV_SHA")
+  NEW_BASE=$(git merge-base origin/main HEAD)
+  if [ "$OLD_BASE" = "$NEW_BASE" ]; then
+    echo "Generating incremental diff from ${PREV_SHA} to HEAD"
+    git diff "${PREV_SHA}..HEAD" > pr.diff
+    echo "incremental=true" >> "$GITHUB_OUTPUT"
+  else
+    echo "PR base changed (merge/rebase from main) — generating full diff"
+    git diff origin/main...HEAD > pr.diff
+    echo "incremental=false" >> "$GITHUB_OUTPUT"
+  fi
 else
   echo "Generating full diff from origin/main to HEAD"
   git diff origin/main...HEAD > pr.diff