I think we need more information here. I can’t understand why you think reattaching the body shell to it’s chassis could crack or break the body shell?? Normally the body slips onto the chassis, it may snap into place also, and then is held in place by some screws. Are you saying the screws are “stiff and tight”??. If so, it may be that some paint got in the holes. You should still be able to screw in the screws, but I suppose you could take a sharp hobby knife with a pointed blade (like an X-acto no.5) and clean some paint out of the holes.
As mentioned, would be rather helpful as to the make of the engine. The plastic won’t shrink, or shouldn’t shrink to cause a shell not to fit. There are a few rare cases, one The Kato NW2 for example. When new the shell will wiggle off the extremely tight/ shoehorned fit and off the retaining “nubs”. As they age and the plastic becomes less pliable the shell is a real bear to remove. I would also imagine if left off could be difficult to install. Now I don’t know if this is the case or way too much paint found it’s way into the shell sides? Examine where the interference is and it may be possible to sand, scrap or otherwise gain the clearance needed. . Do also check that any wiring is routed in any of the slots/ channels as this will cause shell interference as well.