Please help! Original Files moved to Recycle Bin

[UliPhoto]

I'm using FFS for some month now and have to relalise that there must be a serious issue in the way I'm using it or in the way it works. The reason is that loads of original files have been moved to the Windows recylce bin (from the FFS temp recycle bin. I realsised this by coincidence and there is no pattern or outside reason that I can refer to. Possibly there is but I need help.
I have set up FFS with a batch run to synch all files with a NAS drive connected to my Fritzbox. This seemed to work perfectly fine except for the fact that for whatever reason original files have been deleted - and luckily kept in the sync desitination. I searched the Forum and found similar cases and it was referred that there must be an outside FFS reasons for the issue which I can't see in my case. My computer is connected to the network via WLAN and I'm using a little batch job at the startup of the Win7 to make sure the NAS drive is connected. Is this an issue if FFS starts before the destination drive is properly connected or if the WLAN connection is interrupted during sync?