Windows Folder Security Permissions Overwriting Due to Sage 100 Contractor

Support is being unhelpful and blaming a corrupted company file. It has zero to do with ANY of the company files. Whenever you run a Company Payroll Archive from the Database Administration tool the folder security permissions on the company folder are overwritten with whatever user account the MSSQL$SAGE100CON instance is using to start. I am unsure why Sage programmed this in. Support says this is normal. It is not normal. It is OVERWRITING, NOT appending permissions. When the folder permissions are overwritten all users lose access to the folder shares because, you guessed it, Sage removed their access. To me, this seems like a bug and needs to be rectified immediately. Client is running the most recent version of the software.