Folders from PC to Server Share

I (almost) completely disagree - Roaming profiles are HORRIBLE.  They potentially slow logon and logout and can, in GENERALLY rare but NOT NON-EXISTENT circumstances, cause data loss.

For roaming data, use Folder Redirection (for everyone - but watch the group policy setting for permissions or you can have a nightmare of a time gaining access when needed - even virus scanning).  Or if you don't want to, specify a "home drive" in the AD account profiles and store the files there.

As for permissions, as a general rule, NEVER set a user account to the permissions of a file or folder (or share).  The exception is ALMOST always home drives.  Use groups.  Adding and removing users to groups does not require adjusting permissions on all files like use single accounts would (which can be a time consuming and disk intensive operation).  Further, I always add the System account and Domain Admins to the list of users with Full Control rights.  (If you're domain admins are not trustworthy, they shouldn't be your domain admins).  And system is generally necessary for a variety of tasks.

As for merging the folders - Copy one into the other and then copy the combined folder to the server.  Then MOVE the folders on each workstation to a temporary location as BACKUPS (don't tell the user where - you don't want them using them locally when you're trying to put them on the server.

More info on Folder Redirection: https://technet.microsoft.com/en-us/library/cc732275.aspx

I'm with Lee W: I wouldn't use roaming profiles on a PC. I'd go with folder redirection.

The roaming profile vs. folder redirection argument is not new, and there are potential gotchas for both.  For instance, folder redirection would not be ideal if used by applications that hard code the profile path.  The OP should research both and choose the one that works best for their specific environment.

In this case, that's not what's happening based on what I'm reading.

And few apps use that kind of bad coding, thankfully.