How to prevent loss of data when redirecting C:/drive to users home drive

I need to re-enable a GPO to redirect my users C:/drive so they save all of their documents to their home drives on our file server.  A contractor who was here previously turned this GPO off and I wasn't aware of it.  How can I do this with out my users possibly having their files over written?   I don't want older versions of a document over writting a newer version just because I am moving the location where it is stored.  

We also use roaming profiles here.  Some of my roaming profiles are not removed from the machines when they log off leaving some sensitive documents available for others to see when they log on the machine afterwards.  Is this due to the security on the profiles?  This is the only thing that I could come up with.  I am finding this on machines that I have that are still FAT32.  I am changing the ones that I find to NTFS so I can control the security on the profiles and remove the everyone access.  But it is going to take some time for me to check all 500 profiles.  I have only been here a short time and I am finding that things weren't always done in the best way.

Any suggestions on these two matters would be greatly appreciated.  My director is going on vacation Friday.  If I could get these two things fixed or half way fixed before that; I could get some big points before he leaves.

Thanks!!