diff --git a/builtin/merge.c b/builtin/merge.c
index 02a87430f48f97..d023c4d691c765 100644
--- a/builtin/merge.c
+++ b/builtin/merge.c
@@ -371,6 +371,9 @@ static int save_state(struct object_id *stash)
 		die(_("not a valid object: %s"), buffer.buf);
 	rc = 0;
 out:
+	discard_index(the_repository->index);
+	if (repo_read_index(the_repository) < 0)
+		die(_("could not read index"));
 	strbuf_release(&buffer);
 	return rc;
 }
diff --git a/builtin/stash.c b/builtin/stash.c
index 170024c4940b59..7bb0b446844b62 100644
--- a/builtin/stash.c
+++ b/builtin/stash.c
@@ -33,6 +33,7 @@
 #include "add-interactive.h"
 #include "oid-array.h"
 #include "commit.h"
+#include "virtualfilesystem.h"
 
 #define INCLUDE_ALL_FILES 2
 
@@ -1285,9 +1286,10 @@ static int check_changes_tracked_files(const struct pathspec *ps)
 static int check_changes(const struct pathspec *ps, int include_untracked,
 			 struct strbuf *untracked_files)
 {
-	int ret = 0;
-	if (check_changes_tracked_files(ps))
-		ret = 1;
+	int ret = check_changes_tracked_files(ps);
+
+	if (ret < 0)
+		return ret;
 
 	if (include_untracked && get_untracked_files(ps, include_untracked,
 						     untracked_files))
@@ -1296,6 +1298,24 @@ static int check_changes(const struct pathspec *ps, int include_untracked,
 	return ret;
 }
 
+static int check_tracked_files_accessible(const struct pathspec *ps)
+{
+	struct index_state *istate = the_repository->index;
+	struct stat st;
+
+	for (size_t i = 0; i < istate->cache_nr; i++) {
+		struct cache_entry *ce = istate->cache[i];
+
+		if (ce_stage(ce) || ce_skip_worktree(ce) ||
+		    !ce_path_match(istate, ce, ps, NULL))
+			continue;
+		if (lstat(ce->name, &st) < 0 &&
+		    errno != ENOENT && errno != ENOTDIR)
+			return error_errno(_("cannot stat '%s'"), ce->name);
+	}
+	return 0;
+}
+
 static int save_untracked_files(struct stash_info *info, struct strbuf *msg,
 				struct strbuf *files)
 {
@@ -1521,9 +1541,30 @@ static int do_create_stash(const struct pathspec *ps, struct strbuf *stash_msg_b
 	prepare_fallback_ident("git stash", "git@stash");
 
 	repo_read_index_preload(the_repository, NULL, 0);
-	if (repo_refresh_and_write_index(the_repository, REFRESH_QUIET, 0, 0,
-					 NULL, NULL, NULL) < 0) {
-		ret = error(_("could not write index"));
+	ret = repo_refresh_and_write_index(the_repository,
+					   REFRESH_QUIET |
+					   REFRESH_FAIL_ON_STAT_ERROR,
+					   0, 0, NULL, NULL, NULL);
+	if (ret) {
+		ret = error(ret < 0 ?
+			    _("could not write index") :
+			    _("could not refresh index"));
+		goto done;
+	}
+
+	free_virtualfilesystem();
+	enable_fscache(0);
+	flush_fscache();
+	discard_index(the_repository->index);
+	if (repo_read_index(the_repository) < 0) {
+		ret = error(_("could not read index"));
+		goto done;
+	}
+	for (size_t i = 0; i < the_repository->index->cache_nr; i++)
+		the_repository->index->cache[i]->ce_flags &=
+			~(CE_UPTODATE | CE_FSMONITOR_VALID);
+	if (check_tracked_files_accessible(ps) < 0) {
+		ret = -1;
 		goto done;
 	}
 
@@ -1542,10 +1583,8 @@ static int do_create_stash(const struct pathspec *ps, struct strbuf *stash_msg_b
 		}
 	}
 
-	if (!check_changes(ps, include_untracked, &untracked_files)) {
-		ret = 1;
-		goto done;
-	}
+	if (include_untracked)
+		get_untracked_files(ps, include_untracked, &untracked_files);
 
 	branch_ref = refs_resolve_ref_unsafe(get_main_ref_store(the_repository),
 					     "HEAD", 0, NULL, &flags);
@@ -1731,11 +1770,15 @@ static int do_push_stash(const struct pathspec *ps, const char *stash_msg, int q
 		goto done;
 	}
 
-	if (!check_changes(ps, include_untracked, &untracked_files)) {
+	ret = check_changes(ps, include_untracked, &untracked_files);
+	if (ret < 0)
+		goto done;
+	if (!ret) {
 		if (!quiet)
 			printf_ln(_("No local changes to save"));
 		goto done;
 	}
+	ret = 0;
 
 	if (!refs_reflog_exists(get_main_ref_store(the_repository), ref_stash) && do_clear_stash()) {
 		ret = -1;
diff --git a/read-cache-ll.h b/read-cache-ll.h
index 31fa370e43d379..851276d99c3e24 100644
--- a/read-cache-ll.h
+++ b/read-cache-ll.h
@@ -457,6 +457,8 @@ int fake_lstat(const struct cache_entry *ce, struct stat *st);
 #define REFRESH_IN_PORCELAIN             (1 << 5) /* user friendly output, not "needs update" */
 #define REFRESH_PROGRESS                 (1 << 6) /* show progress bar if stderr is tty */
 #define REFRESH_IGNORE_SKIP_WORKTREE     (1 << 7) /* ignore skip_worktree entries */
+/* Report unexpected stat errors even when REFRESH_QUIET is set. */
+#define REFRESH_FAIL_ON_STAT_ERROR       (1 << 8)
 int refresh_index(struct index_state *, unsigned int flags, const struct pathspec *pathspec, char *seen, const char *header_msg);
 /*
  * Refresh the index and write it to disk.
diff --git a/read-cache.c b/read-cache.c
index 7653d13fa36e6f..360a8806a80648 100644
--- a/read-cache.c
+++ b/read-cache.c
@@ -1508,6 +1508,7 @@ int refresh_index(struct index_state *istate, unsigned int flags,
 	int not_new = (flags & REFRESH_IGNORE_MISSING) != 0;
 	int ignore_submodules = (flags & REFRESH_IGNORE_SUBMODULES) != 0;
 	int ignore_skip_worktree = (flags & REFRESH_IGNORE_SKIP_WORKTREE) != 0;
+	int fail_on_stat_error = (flags & REFRESH_FAIL_ON_STAT_ERROR) != 0;
 	int first = 1;
 	int in_porcelain = (flags & REFRESH_IN_PORCELAIN);
 	unsigned int options = (CE_MATCH_REFRESH |
@@ -1603,8 +1604,13 @@ int refresh_index(struct index_state *istate, unsigned int flags,
 				mark_fsmonitor_invalid(istate, ce);
 				istate->cache_changed |= CE_ENTRY_CHANGED;
 			}
-			if (quiet)
+			if (quiet) {
+				if (fail_on_stat_error &&
+				    cache_errno != EINVAL &&
+				    cache_errno != ENOENT)
+					has_errors = 1;
 				continue;
+			}
 
 			if (cache_errno == ENOENT)
 				fmt = deleted_fmt;
diff --git a/t/t3903-stash.sh b/t/t3903-stash.sh
index 4b306010053bcd..0a02f1ac1fd34c 100755
--- a/t/t3903-stash.sh
+++ b/t/t3903-stash.sh
@@ -640,6 +640,82 @@ test_expect_success 'stash create - no changes' '
 	test_must_be_empty actual
 '
 
+test_expect_success 'stash create - clean after index refresh' '
+	test_create_repo create-refresh-race &&
+	(
+		cd create-refresh-race &&
+		test_commit A file &&
+		write_script .git/hooks/post-index-change <<-\EOF &&
+		if test ! -e .git/hook-fired
+		then
+			>.git/hook-fired
+			test-tool chmtime -3600 file
+		fi
+		EOF
+
+		# The first check sees a stat change. The hook changes only
+		# the mtime after refresh, so the stash tree remains clean.
+		test-tool chmtime +3600 file &&
+		git stash create >actual &&
+		test_file_not_empty actual &&
+		test_cmp_rev "$(cat actual)^{tree}" HEAD^{tree} &&
+		test_path_is_file .git/hook-fired
+	)
+'
+
+test_expect_success 'stash create - captures worktree changes during refresh' '
+	test_create_repo create-content-race &&
+	(
+		cd create-content-race &&
+		test_commit A file &&
+		write_script .git/hooks/post-index-change <<-\EOF &&
+		if test ! -e .git/hook-fired
+		then
+			>.git/hook-fired
+			echo changed >file
+		fi
+		EOF
+
+		# A content change after refresh must be included in the stash.
+		test-tool chmtime +3600 file &&
+		git stash create >actual &&
+		git show "$(cat actual):file" >stashed &&
+		test_cmp file stashed &&
+		git diff --exit-code --cached &&
+		test "changed" = "$(cat file)"
+	)
+'
+
+test_expect_success 'stash create - reloads virtual filesystem paths' '
+	test_create_repo create-vfs-race &&
+	(
+		cd create-vfs-race &&
+		echo visible >visible &&
+		echo original >hidden &&
+		git add visible hidden &&
+		git commit -m initial &&
+		printf "visible\0" >.git/vfs-paths &&
+		write_script .git/hooks/virtualfilesystem <<-\EOF &&
+		cat .git/vfs-paths
+		EOF
+		git config core.virtualfilesystem \
+			.git/hooks/virtualfilesystem &&
+		write_script .git/hooks/post-index-change <<-\EOF &&
+		if test ! -e .git/hook-fired
+		then
+			>.git/hook-fired
+			echo changed >hidden
+			printf "visible\0hidden\0" >.git/vfs-paths
+		fi
+		EOF
+
+		test-tool chmtime +3600 visible &&
+		git stash create >actual &&
+		git show "$(cat actual):hidden" >stashed &&
+		test_cmp hidden stashed
+	)
+'
+
 test_expect_success 'stash branch - no stashes on stack, stash-like argument' '
 	git stash clear &&
 	test_when_finished "git reset --hard HEAD" &&
diff --git a/t/t7600-merge.sh b/t/t7600-merge.sh
index 64fe21717db0d4..aa76a3a27dadd9 100755
--- a/t/t7600-merge.sh
+++ b/t/t7600-merge.sh
@@ -1179,4 +1179,83 @@ test_expect_success 'merge with no argument defaults to upstream' '
 	)
 '
 
+test_expect_success 'merge accepts a stash created after index refresh' '
+	test_create_repo merge-refresh &&
+	(
+		cd merge-refresh &&
+		echo unchanged >victim &&
+		echo base >base &&
+		git add base victim &&
+		git commit -m base &&
+		git branch -M main &&
+
+		git checkout -b side &&
+		echo side >side &&
+		git add side &&
+		git commit -m side &&
+
+		git checkout main &&
+		echo main >main &&
+		git add main &&
+		git commit -m main &&
+
+		write_script .git/hooks/post-index-change <<-\EOF &&
+		if test ! -e .git/hook-fired
+		then
+			>.git/hook-fired
+			test-tool chmtime -3600 victim
+		fi
+		EOF
+
+		test-tool chmtime +3600 victim &&
+		git merge side &&
+		test_path_is_file side &&
+		test_path_is_file .git/hook-fired
+	)
+'
+
+test_expect_success 'merge autostash creates a stash after refresh' '
+	test_create_repo merge-autostash-refresh &&
+	(
+		cd merge-autostash-refresh &&
+		echo original >victim &&
+		echo trigger >trigger &&
+		echo base >base &&
+		git add base trigger victim &&
+		git commit -m base &&
+		git branch -M main &&
+
+		git checkout -b side &&
+		echo side >side &&
+		git add side &&
+		git commit -m side &&
+
+		git checkout main &&
+		echo main >main &&
+		git add main &&
+		git commit -m main &&
+		cp victim .git/victim-clean &&
+		echo changed >victim &&
+
+		write_script .git/hooks/post-index-change <<-\EOF &&
+		count=$(cat .git/hook-count 2>/dev/null || echo 0)
+		count=$((count + 1))
+		echo $count >.git/hook-count
+		if test $count -eq 1
+		then
+			test-tool chmtime -3600 trigger
+		elif test $count -eq 2
+		then
+			cp .git/victim-clean victim
+		fi
+		EOF
+
+		test-tool chmtime +3600 trigger &&
+		git merge --autostash side &&
+		test_path_is_file side &&
+		test_cmp .git/victim-clean victim &&
+		test "$(cat .git/hook-count)" -ge 2
+	)
+'
+
 test_done