Your receiver should not void audyssey and DEQ settings if you lower the crossover. I think you didn't run it properly or else it wouldn't cross your speakers this high (200Hz). If they are rated to 110Hz, you should be able to cross them at 120Hz. See Audyssey FAQ.
No effect as long as you are using LFE input, which bypasses a sub's internal xo.
No effect as long as you are using LFE input, which bypasses a sub's internal xo.