Welcome to the community, @Markus_Sullivan! Thanks for reaching out. 
I've not seen this before and am successfully able to publish a converted app that contains SQL queries, but am happy to dig into it with you. Quick point of clarification about your use of the term "backend", though - is your classic app utilizing an app function or isolated resource query? We paused development on the former earlier this year and I wouldn't necessarily expect it to be convertible.
You mention sharing a minimal repro - any additional context would be super helpful! Alternatively, you are welcome to join our scheduled Office Hours.