diff --git a/scripts/commit.sh b/scripts/commit.sh
index 04f57c1..ae4ff3a 100644
--- a/scripts/commit.sh
+++ b/scripts/commit.sh
@@ -902,6 +902,23 @@ function _stage_file_by_status {
     esac
 }
 
+### Stage a split group exactly as it was in the original index: each path
+### gets its entry from the pre-split tree (or is removed when the tree has
+### none). Unlike re-adding the worktree copy this keeps partially staged
+### hunks, and works for staged files since deleted from the worktree.
+# $1: tree of the original index (git write-tree)
+# $2..: files of the group
+# Prints git's error on stderr and returns non-zero on failure.
+function _stage_split_group_from_tree {
+    local tree="$1"; shift
+    local -a pathspecs=()
+    local f
+    for f in "$@"; do
+        pathspecs+=(":(top,literal)$f")
+    done
+    git restore --staged --source="$tree" -- "${pathspecs[@]}" 2>&1 >/dev/null
+}
+
 ### Capture the change type for each currently-staged file into a map.
 # Sets the global associative array `_split_status_by_file` (file → A/M/D/...).
 # For renames/copies (R, C), git emits the new path as the second field — we
@@ -1238,18 +1255,31 @@ function perform_commit_split {
         # Stage each file using the original change type so deletions stay
         # deletions (otherwise `git add` would re-add the worktree copy and
         # the index ends up empty for that scope, breaking AI generation).
-        local stage_failed=0
+        # Prefer the original index tree: it is exact (partial hunks, staged
+        # files since removed from the worktree). The per-file replay is the
+        # fallback when the tree could not be captured.
+        local stage_failed=0 stage_err=""
         local _stage_status
-        for f in "${files_array[@]}"; do
-            _stage_status=$(gmap_get _split_status_by_file "$f"); [ -z "$_stage_status" ] && _stage_status="M"
-            if ! _stage_file_by_status "$f" "$_stage_status"; then
-                stage_failed=1
-                break
-            fi
-        done
+        if [ -n "$orig_tree" ]; then
+            stage_err=$(_stage_split_group_from_tree "$orig_tree" "${files_array[@]}") || stage_failed=1
+        else
+            for f in "${files_array[@]}"; do
+                _stage_status=$(gmap_get _split_status_by_file "$f"); [ -z "$_stage_status" ] && _stage_status="M"
+                if ! stage_err=$(_stage_file_by_status "$f" "$_stage_status" 2>&1); then
+                    stage_failed=1
+                    break
+                fi
+            done
+        fi
         if [ "$stage_failed" = "1" ]; then
             echo -e "${RED}✗ Cannot stage files for scope '${scope}'.${ENDCOLOR}"
-            _restore_split_snapshot "$snapshot_file"
+            [ -n "$stage_err" ] && echo -e "${GRAY}${stage_err}${ENDCOLOR}"
+            if [ -n "$orig_tree" ] && git read-tree "$orig_tree" >/dev/null 2>&1; then
+                rm -f "$snapshot_file"
+            else
+                _restore_split_snapshot "$snapshot_file"
+            fi
+            echo -e "${YELLOW}Original staging restored.${ENDCOLOR}"
             trap - INT TERM
             return 1
         fi
@@ -1539,9 +1569,13 @@ function try_offer_commit_split {
         fi
     fi
 
+    local grouped_with_ai=""
     if [ "$should_use_ai" = "true" ] && check_ai_available 2>/dev/null; then
         echo
         echo -e "${YELLOW}Grouping changes by feature with AI...${ENDCOLOR}"
+        # Keep the spinner off the header line, like the other progress views.
+        echo
+        grouped_with_ai="true"
         local ai_grouping_fail_reason=""
         if ! group_files_by_feature_with_ai; then
             # AI failed; keep the folder heuristic groups (may be empty). Surface
@@ -1568,7 +1602,8 @@ function try_offer_commit_split {
     # split commits don't reference code that history hasn't introduced yet.
     order_split_groups_by_dependency
 
-    echo
+    # The AI grouping header already left a blank line.
+    if [ -z "$grouped_with_ai" ]; then echo; fi
     print_split_groups_preview
     echo
 
diff --git a/tests/test_commit_split_integrity.bats b/tests/test_commit_split_integrity.bats
index f4660fb..f6c1e5d 100644
--- a/tests/test_commit_split_integrity.bats
+++ b/tests/test_commit_split_integrity.bats
@@ -169,3 +169,40 @@ teardown() {
     [ "$(git rev-parse HEAD)" = "$start_head" ]
     [ "$(git write-tree)" = "$orig_tree" ]
 }
+
+@test "perform_commit_split: commits the staged content, even for files gone from the worktree" {
+    mkdir -p docs scripts
+    echo "base" > docs/a.md
+    echo "base" > scripts/b.sh
+    git add docs/a.md scripts/b.sh
+    git commit -q -m "seed"
+
+    echo "staged" > docs/a.md
+    echo "new" > docs/new.md
+    echo "changed" > scripts/b.sh
+    git add docs/a.md docs/new.md scripts/b.sh
+    # Unstaged edits and a staged file deleted from the worktree: re-adding
+    # the worktree copy would commit the wrong content or fail outright.
+    echo "unstaged-extra" >> docs/a.md
+    rm docs/new.md
+
+    gmap_clear split_groups
+    gmap_set split_groups "docs" "docs/a.md"$'\n'"docs/new.md"
+    gmap_set split_groups "scripts" "scripts/b.sh"
+    split_group_keys=(docs scripts)
+    llm="true"
+    auto_accept="true"
+    push=""
+    current_branch="main"
+    check_ai_available() { return 0; }
+    generate_ai_commit_message() { echo "chore: ai message"; }
+
+    run perform_commit_split
+
+    [ "$status" -eq 0 ]
+    [[ "$output" != *"Cannot stage files"* ]]
+    [ "$(git show HEAD~1:docs/a.md)" = "staged" ]
+    [ "$(git show HEAD~1:docs/new.md)" = "new" ]
+    [ "$(git show HEAD:scripts/b.sh)" = "changed" ]
+    [ -z "$(git diff --cached --name-only)" ]
+}