We removed a ceiling fan that was installed on a pancake box that is mounted directly to the joists in the ceiling/attic. The bolt on the new chandelier is too long to be fit inside the pancake box and have the canopy rest flush to the ceiling. We considered cutting the threaded bolt that the wires pull through but we'd have to cut it so short it felt like there may be another option?
My suggestion is to find a different fan rated pancake that does not have the mounting holes directly inline with the beam. Alternatively, go buy a new pancake and drill holes to mount it where the holes aren't inline with the beam.
Either suggestion shouldn't cost you much.
I installed an old style, heavy Hunter fan using a pancake box directly under the ceiling joist/rafter in a vaulted ceiling. The fan was hung from a heavy hook which was screwed into the 2x12" joist through the center hole in the pancake box. This was NOT a bolt going all the way through with a washer and nut on the other side, but a screw hook which came with the fan.
In rooms with 8' ceilings I put in 2x4" blocking between the bottom cords of the trusses (which serve as ceiling joists) and screwed the hooks into that. This allowed exact centering of the fans in the room and distributed the weight between two 2x4 ceiling joists. I believe I could have screwed directly into a bottom cord, but wanted to be extra careful to distribute the weight of these heavy fans.
If your chandelier has a hook and you need an EYE, just get one of the proper size and drill a suitable pilot hole. I lubed the threads with wax, but other lubes are possible--soap, silicone grease, etc.
EDIT An admission: our 48 year old tract house, which we have lived in since 1978, had a chandelier over the dining room table, rather light weight and not attractive.
Five years or so ago my wife bought a significantly heavier chandelier (15 lb?), made in China, which I just hung from the original ceiling box with the parts supplied. I can't even remember how I did it, but probably with two screws into holes in the fiber plastic box which I think is side nailed into the 2 x 12" rafter/ceiling joist of a vaulted ceiling. Probably a central hollow rod screws into a metal strap which is held by the two screws.