I saw a command on your site that showed when the last time a system/directories/files were saved. Running this command would get you a report to show this information. Do you remember it, or have any suggestions to retrieve this kind of information?
All QSF and QMF save files should be deleted by the system when PTFs are permanently applied. You should not delete them manually. If after you have applied the PTFs permanently and they still remain on your system, there may be a problem. I would suggest that you contact IBM Software Support for assistance.