This has been resolved - in case anyone else comes across this same error. It was an issue with the database. We had forgot to upgrade it (“make upgrade-database”) (documentation)
I got it working. I was moving from one system to another.
I did a make initialize-database, then I restored a dump from the existing, then I ran the make upgrade-database
The error likely stems from performance issues due to more complex or inefficient queries after the RT upgrade. To fix it, try optimizing your queries or increasing the maximum runtime in the RT configuration. Consult your RT admin to adjust these settings as needed.