Can you provide a screenshot of the workflow with the transitions back to the appropriate state? (maybe a cex file (export) is better).
If it is proprietary, you can email it to me. I just want to understand the level of complexity before I suggest what I'm thinking...
Are they a specific varible filled out when the files was created because if those files does have a variable you can let that be a filter for the file to automatically move through another workflow:
Or you could have a transistion that would go from one workflow to a specific state in another workflow and then move the files (I have not tested this but it should work)
So they would still have to change state on the file and then move them. but it would solve your issue and you would write some variables in that transistion that this project from from XXXXX state XXX user did this transistion etc. just to keep track of things.