I wrote "What was in the suitcase František HAD forgotten?" and it was rejected. My idea was, that František's forgetting happened some time before someone noticed it and then, later, asked about it.
I will add it.
Could this be interpreted as "what object frantisek forgot to put in the suitcase"? Now I understand it as "I want to know what was inside the suitcase" But I originally though it meant "frantisek forgot something in the suitcase, what was it".
No, it cannot. You can use "Co (to) František zapomněl v tom kufru?." Or if you insist on complicating it with a compound sentence: "Co byla ta věc, již František zapomněl v tom kufru?".