Even Lukas Eder, the creator of JOOQ, suggests to use Hibernate for CRUD and JOOQ for querying:
https://blog.jooq.org/2015/03/24/jooq-vs-hibernate-when-to-c...
My models have always been fairly simple with not too many levels of child entities. I contain all the logic for a given entity in a single class (where I hand write the code to update related entities). I do have to keep my fingers crossed that nobody will implement similar-but-wrong logic in some other spot in the codebase. The 1:1 mapping between entities and classes to CRUD helps to some degree.
I use jOOQ as well, but mostly only for the reading part. For the above case, I still use Hibernate, as I've yet to find an efficient way to do it in jOOQ.