[BUG] Homestead support papers in use suddenly gone and all plots unclaimed except the base 16

What type of papers were used? Homestead support papers for example cannot be used in a homestead that is part of any settlement.

Well, without a reproduction case I cannot really say what happened - the homestead support papers should indeed only be removed when you actually join the country (and you get a warning about that then, in case of annexation it's different but they need to give you country papers for it).

What also could have happened is that the town you got the homestead support papers from shrinked or dissolved, in either case it maybe was no longer able to support the amount of papers, but you'd get a warning then as well.