Uploaded files are considered temporary and will be removed by cleanup_database.pl unless an authorised value from category UPLOAD is provided. By default, Koha sets empty category meaning the uploaded file is considered a temporary upload. Add a system preference to define an upload category to be selected by default.
Since not everyone likes adding yet another system preference, one option would be to select the most used category by default. Btw by selecting I mean values for the "Category" dropdown under Tools -> Upload (requires at least one authorised_value under UPLOAD category to display the dropdown)
Adding a few notes, > will be removed by cleanup_database.pl unless an authorised value from category UPLOAD is provided. cleanup_database.pl only removes temporary files if system preference "UploadPurgeTemporaryFilesDays" is set. > By default, Koha sets empty category meaning the uploaded file is considered a temporary upload. Technically Koha only looks at uploaded_files.permanent flag for temporary file deletion.