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POPSVocabulary permissions module suffers from a "Drupal limitation" "User A creates a node and applies some terms from various vocabs. Now, user B comes along and edits the node. But user B has some vocabs removed from his node edit page by your module. Now when user B submits the node form Drupal removes ALL terms in ALL vocabs, then re-adds them. However, it cannot "re-add" terms that you didn't allow user B to have. So, effectively user B has managed to deleted terms in vocabs she didn't have access to."