Data Integrity: laboratory systems

Dear all,

Many of the software that controls laboratory equipment uses file storage in folders (Windows based) instead of using somekind of database storage. Both the health Authorities and the Clients are becoming more and more aware of this issue and start questioning the controls in place to ensure data protection and integrity.
As you know, every software that is Windows based, allow deletion of files from the folders outside the software, without any kind of record of that action in the software audit trail.

So my question is, in that case what are the means you have to protect your files?