FYI we’ve used this approach for payu for a number of years and it has worked fine. As long as you set shortpath you should be able to change the project and still pick up previous restarts from the same location, and write outputs there.
One little trick to consider is to use setgid to ensure all files are written with the same project code as the shortpath project location
Note that this will mean setting chmod +s for the work and archive subdirectories in the shortpath/$USER/$MODEL directory.