I'm interested in strategies for this as well.
It does seem like a complicated problem for a full export/import process. Aside from the obvious project/subject/session/scan/resource, etc. hierarchy, you might want to retain users, project settings, custom forms, custom datatypes, event service subscriptions, commands, etc, etc. any/all of which might need to be restored/recreated on import, if altered or removed after your export.
I'm guessing the simplest strategy is to just move the project's data off to cold storage, leave the project's shell in place on the filesystem and in XNAT and just remove user access?