We have seen cases today (April 17) where someone changed user permissions in the registry, and then the updated permissions file in the project is invalid because of bad book IDs. Paratext will say there was a problem reading permissions because of bad Book IDs. The developers have been notified and are working on the problem. But in the meantime, it would be smart not to change permissions (add users, modify user roles, remove users) in the registry, but to modify permissions only in Paratext. Hopefully this will be fixed soon.
Update: April 18: A fix was applied to the server several hours ago.