I've frequently noticed when switching between trees that "admin" account switches back to its default password, and my more limited user accounts disappear and need to be recreated.
Global users are stored in the .basexperm file, while local permissions will be stored in the meta file of a database (inf.basex).
I didn't come across this issue before.. Do you have a reproducible example?
Thanks, Christian
PS: sorry for delaying your other mails; seems this is getting a very busy week.