Change Flow Target - Detecting Changed Files

I am currently using the 'Change Flow Target' option within RTC to handle the synchronisation of change sets between multiple streams (in particular I am using this functionality to handle the back-porting of code fixes to older releases of the source code).

Unfortunately I made a mistake at one point and dropped a large number of files into one of the older streams.  I reversed these file changes, but I now get conflicts whenever I change the flow target back to this older stream, even when there are no actual differences in the files themselves.

How does Jazz work out whether a conflict exists?  Does it purely use the history of the file, or does it use some other mechanism?

Is there a way to manually re-sync these files so that I don't get these unnecessary conflicts whenever I change the flow target? 

Thanks,

Scott.