Tested versions

• Godot 4.4.1-stable

System information

Macos Sequoia 15.5

Issue description

I added a a scene file inside the POT generation file list
Once I deleted the file inside Godot, the deleted scene is still present inside POT file list

Steps to reproduce

Add a scene file into POT generation list
Delete scene inside project files
Scene file is still present inside POT file list

Minimal reproduction project (MRP)

Don't have a minimal project to reproduce, mine is 4 years old ...