A quick though on this…
You could move this logic into an orchestration.
Using the context properties of the message you could identify where the source file arrived from and write out your .flag file to this location. For this, I believe that you could use the File Adapter in a send port.
Do your processing…
Once complete you would then write out the .done file. This could as well be done using the File Adapter in a send port.
I believe that to delete your .flag file you will need to do this using an expression shape that deletes the file. There are other ways to do this last one, but i am not currently aware of anyway to rename a file in a directory using the native biztalk adapters.