diff --git a/.github/actions/composite/updateProtectedBranch/action.yml b/.github/actions/composite/updateProtectedBranch/action.yml
index 9c7b4ea0c8fb..892c6cd27eca 100644
--- a/.github/actions/composite/updateProtectedBranch/action.yml
+++ b/.github/actions/composite/updateProtectedBranch/action.yml
@@ -53,7 +53,9 @@ runs:
 
     - name: Checkout source branch
       shell: bash
-      run: git checkout ${{ env.SOURCE_BRANCH }}
+      run: |
+        git fetch
+        git checkout ${{ env.SOURCE_BRANCH }}
 
     - name: Set New Version
       shell: bash
@@ -66,7 +68,10 @@ runs:
         git checkout ${{ inputs.TARGET_BRANCH }}
         BRANCH_NAME=update-${{ inputs.TARGET_BRANCH }}-from-${{ env.SOURCE_BRANCH }}
         git checkout -b "$BRANCH_NAME"
-        git merge -Xtheirs ${{ env.SOURCE_BRANCH }}
+        git merge -Xtheirs ${{ env.SOURCE_BRANCH }} || {
+          git diff --name-only --diff-filter=U | xargs git rm;
+          git merge --continue;
+        }
         git push --set-upstream origin "$BRANCH_NAME"
 
     - name: Create Pull Request
diff --git a/tests/unit/getPullRequestsMergedBetweenTest.sh b/tests/unit/getPullRequestsMergedBetweenTest.sh
index 47e0e9d9c351..84c29d333bff 100755
--- a/tests/unit/getPullRequestsMergedBetweenTest.sh
+++ b/tests/unit/getPullRequestsMergedBetweenTest.sh
@@ -117,7 +117,7 @@ success "Version bumped to $(print_version) on main"
 info "Merging main into staging..."
 git checkout staging
 git checkout -b update-staging-from-main
-git merge --no-edit -Xtheirs main
+git merge --no-edit -Xtheirs main || { git diff --name-only --diff-filter=U | xargs git rm; git merge --continue; }
 git checkout staging
 git merge update-staging-from-main --no-ff -m "Merge pull request #3 from Expensify/update-staging-from-main"
 info "Merged PR #3 to staging"
@@ -219,7 +219,7 @@ title "Scenario #4A: Run the production deploy"
 info "Updating production from staging..."
 git checkout production
 git checkout -b update-production-from-staging
-git merge --no-edit -Xtheirs staging
+git merge --no-edit -Xtheirs staging || { git diff --name-only --diff-filter=U | xargs git rm; git merge --continue; }
 git checkout production
 git merge update-production-from-staging --no-ff -m "Merge pull request #8 from Expensify/update-production-from-staging"
 info "Merged PR #8 into production"
@@ -250,7 +250,7 @@ success "Successfully updated version to 1.1.0 on main!"
 info "Updating staging from main..."
 git checkout staging
 git checkout -b update-staging-from-main
-git merge --no-edit -Xtheirs main
+git merge --no-edit -Xtheirs main || { git diff --name-only --diff-filter=U | xargs git rm; git merge --continue; }
 git checkout staging
 git merge update-staging-from-main --no-ff -m "Merge pull request #10 from Expensify/update-staging-from-main"
 info "Merged PR #10 into staging"
@@ -299,7 +299,7 @@ success "Bumped version to 1.1.1 on main!"
 info "Merging main into staging..."
 git checkout staging
 git checkout -b update-staging-from-main
-git merge --no-edit -Xtheirs main
+git merge --no-edit -Xtheirs main || { git diff --name-only --diff-filter=U | xargs git rm; git merge --continue; }
 git checkout staging
 git merge update-staging-from-main --no-ff -m "Merge pull request #13 from Expensify/update-staging-from-main"
 info "Merged PR #13 into staging"