Why do you need that "work table"? It may be an unavoidable requirement but if you can avoid using it, you avoid this issue.
It's possible to make this work by "tagging" the records created by each user by their account name. Then your scripts and relationships use these tags so that User A sees and deletes on the records tagged with his account name and thus work table records created by User B are left untouched.
Coming from the IBM AS/400 arena, each user has a temporary work folder that is created for them when they log in. They can use this folder for whatever work files they need without worrying about any other user. The folder is deleted when they logoff. Perhaps in a future, future release of FMP...
Thanks, the idea of tagging also occurred to me so will go with it.
What I am describing is, functionally, exactly the same as what you describe with "folders". But such is rarely needed in FileMaker. If you describe how you are trying to use this work table, someone might be able to suggest an alternative approach that does not require using one.