[LyX/master] Fix regression introduced via #12819.

[Pavel Sanda]

commit e322ef153daba01eeb45402b8cf31d32311a3207
Author: Pavel Sanda <sanda at lyx.org>
Date:   Mon Aug 19 22:03:16 2024 +0200

    Fix regression introduced via #12819.
    
    We will mark buffer as modified only in case of removal,
    not when just externally modified.
    
    https://www.mail-archive.com/lyx-devel@lists.lyx.org/msg222715.html
---
 src/Buffer.cpp | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/Buffer.cpp b/src/Buffer.cpp
index 35b45202d1..cdbfe5f0e2 100644
--- a/src/Buffer.cpp
+++ b/src/Buffer.cpp
@@ -5667,7 +5667,6 @@ 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.
@@ -5678,6 +5677,7 @@ 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"