So, why the single folder? I beta tested some of the Connector Workflows along with the BIM360 File Locking utility for AutoCAD and have not had any issues.
A few options for repathing....
1) Reference Manager utility
2) Open each file and manually repath
3) Script/automation and use the XREF command from Lisp to convert them (only works for Xrefs, not Images)
4) Temporarily load into Autodesk Vault as that process converts paths to relative, you can then pull them out and move them to the desktop connector.
5) ...everything else I'm forgetting...