Correct. Metadata are independent. You can change these any time and they will not impact your feature table! In fact, the metadata are intended to be flexible and mutable.
It is the number of distances, not the number of sample. See this post (and the rest of that thread) for more detail.
It sounds like you just mixed up the action you used here: before you used alpha-rarefaction and now you used alpha_group_significance, but this is not really clear from your question (sharing the old/new files would help clarify, but you can really just check the provenance in the files to make sure you used the same action and version of qiime2 to produce them)
No! Everything I have seen so far is looking fine.
Yes. Exporting creates a copy of the file. Your artifact file remains in place.
Good luck!