Depends on the make.
You're not talking about an old Grabow, by any chance, are you?
If you're lucky, you've got yourself an adjustomatic by Grabow. I own a couple and they are designed to be rotated for realignment without harming the pipe.
I had an old Kaywoodie Flame Grain that had a screw in tenon that was almost 180°off when tight. The recommendation I received worked well, I am not sure this would work on all pipes with screw in tendons.
1. Remove stem.
2. Heat tenon with soft flame lighter for several seconds. I stopped when I saw some smoke coming from the base of the stem/tenon junction. No clue if this was almost too hot or perfect.
3. Screw tenon into pipe and if the glue is softened you can now rotate the stem in the same direction as the threads run until the stem is properly indexed.
I think this worked on the old Kaywoodie in part because the metal tenon had a stop or base to the threads to keep the tenon from just screwing further in the pipe and pulling out of the hot glue.
Once things were lined up I let her cool off a bit and the pipe came apart just like normal. The glue does not seem any weaker for the process.
for bone tenons I nuke some water in a glass for a couple minutes and put the stem in (tenon end down) for a few minutes. The heat softens the glue enough to turn the tenon. A bone tenon will usually turn with finger pressure. If it keeps moving around take the tenon out and put a dab of wood glue on it and insert and realign.