Found the solution. So i deployed Retool over a year ago and when i run the update script it doesn't grab all of the latest files and folders vs pulling a fresh install from the git url, i was missing a chunk of data from my docker-compose.yml and other data relating to workflows and retooldb.
Below is a side by side comparison of pulling the latest git on the left side (as of 17th Dec 2023) vs what i had in my retool-onpremise directory on the right side which was originally pulled back in Oct/Nov 2022 and gone through several './update_retool.sh' runs.
If you have the same issue i had then do a fresh install on another test machine and cross check files and folders.