Another update: I seem to have fixed the issue by creating a new release. I got the idea because of some similar posts like this one which suggested to merge branches. I'm not I'm not using git version control for this app but I thought I'd try the release.
I'm still not sure what caused this issue because I was triggering the erroring workflows within the retool edit page with the latest unreleased version (not previewing the app or using the app live with a prior release). But I'm now able to trigger the workflow queries which were failing before release and the original issue of the workflow query not returning data is magically resolved as well.