I apologize for my extended absence, @JulienVDC.
I am at a complete loss as to why uploaded files would be disappearing from the server.
Is it possible that you have backup software running on the server that is restoring an earlier backup on the installation files?
If the files were being restored from a back — but not the database — the result would be exactly this type of behavior.
Failing that, I would have to think about it some more. But I am fairly confident that it isn’t an issue with osTicket Awesome (I suspect that it has something to do with your environment and the same type of thing would be occurring if you were using vanilla osTicket).
Let me know.