And should you not first go to the last 3 version then move to the last 4 version. There you have a lot of cleaning up to do before you can go to 5 (and use the final 5 instead of beta 7). Certainly from 3 to 4 you have to look at all your persisitent create new actions you have to check.
Regards,
Ronald
You can't directly change how the Modeler tries to synchronize with your database.
You can, however, perform the updates yourself (the ones that are giving you issues). Right before synchronizing you have the option to look at the queries it will run.
Find this update script and try running it yourself. It'll either work, or at the very least, give you some more information on what's going on. You can cancel out of the synch after copying down the scripts.
If you get it to work manually, you can redeploy and synchronize again. It won't need to run the script anymore (obviously).
EDIT: By checking out the script it runs, you can see the subquery that is returning more than one record, as the error states. There might be some bad data in your db for some reason. You'll at least understand the issue better.