I have folders setup in the jdownloads directory and they are my categories. When a user makes changes to a file, we would just delete the current file in the folder, then we would add the new file to that same folder. The auto monitoring would show the old file as not found and thus unpublished, and would also see the new file and add that as published.
When we follow this procedure now, it will show the old file as unpublished, but will not see the new file. I do believe that this is because when the old file is deleted, the record still stays in the database and since the filename would remain the same, the database will not allow it. If I delete the database record, the new file is found.
I would like to add that this only started happening after my update to Joomla 3.9.2