Currently (FB6.2.0.1265), using the built-in SCC integration does not play especially well with branches in Team Foundation Server (not sure about other SCC providers).
If I branch a tree containing an FB6 project, then open the FB6 project in the new branch, there's effectively no way to update the SCC bindings to the new path from within FB. The "Refresh Source Control" operation that FB6 does automatically upon project opening transparently creates a new workspace mapping to make the newly branched file appear at it's old location in the SCC tree. Any edits that are made, including removing binding information, is actually done to the file in the old SCC location, not the new location.
In order to successfully use an FB6 file in a new branch, I've found the only workable solution is to check out the file using Team Explorer and manually edit the SCC binding information (e.g. in Visual Studio or Notepad) and only then open it with FB6.
Is there a better way to do this?
One thing that seems like it would help, but it may be behavior of MSSCCI that FB has no control over, is to disable the automatic creation of workspace mappings - if the file system path and the SCC path don't match, assume that the file is not under source control (and display a message), rather than trying to "fix" it.