Hi Jeroen,
I didn't know the records of process entities are removed when the BPT finishes. I have looked it up on the documentation and couldn't find an explicit answer for that question. I can imagine, though, it has to do with the reference to the Process entity and the heavy load of BPT process-related tables, as they record all the BPT instances of the factory along time and the number of records can increase a lot.
Even what I mentioned previously in a scenario where scalability matters should be avoided for the same reason: to avoid queries hitting tables with potential millions of records which support constant activity of the factory.
My suggestion would be to to disable the process entity, create your own entity to store the information you need and use callback actions to populate it. Something along the lines of what is suggested in the Scale Queries over Process Entities documentation.