[LyX/2.4.x] Fix regression introduced via #12819.

[Pavel Sanda]

commit 3a68177562fa4f6cadb27606cdbe92c6f514d78c
Author: Pavel Sanda <sanda at lyx.org>
Date:   Tue Aug 20 09:32:03 2024 +0200

    Fix regression introduced via #12819.
    
    Cherry-pick e322ef153.
---
 src/Buffer.cpp | 2 +-
 status.24x     | 4 ++++
 2 files changed, 5 insertions(+), 1 deletion(-)

diff --git a/src/Buffer.cpp b/src/Buffer.cpp
index b6fd8a3bc3..1dc29d9568 100644
--- a/src/Buffer.cpp
+++ b/src/Buffer.cpp
@@ -5728,7 +5728,6 @@ void Buffer::Impl::fileExternallyModified(bool const exists)
 		       "checksum unchanged: " << filename);
 		return;
 	}
-	lyx_clean = false;
 	// If the file has been deleted, only mark the file as dirty since it is
 	// pointless to prompt for reloading. If later a file is moved into this
 	// location, then the externally modified warning will appear then.
@@ -5739,6 +5738,7 @@ void Buffer::Impl::fileExternallyModified(bool const exists)
 	if (wa_ && wa_->unhide(owner_)) {
 		wa_->updateTitles();
 		if (!exists) {
+			lyx_clean = false;
 			frontend::Alert::warning(
 				_("File deleted from disk"),
 				bformat(_("The file\n  %1$s\n"
diff --git a/status.24x b/status.24x
index a6240f71f9..0263d457a5 100644
--- a/status.24x
+++ b/status.24x
@@ -46,6 +46,10 @@ What's new
 
 - Improve document output pane (bug 12902).
 
+- Fix regression which marks document modified in case of external
+  modification. Only file deletion will trigger the modification
+  flag now (see bug 12819).
+
 
 * DOCUMENTATION AND LOCALIZATION