Answer
Once a base form granted to a permission set is customized, the dictionary now resolves to the customized form by default — so the customized form also needs to be explicitly added to the permission set alongside (or instead of) the original base form, or users lose access even though the base form still shows as granted. For an LTU permission set specifically, IFS's licensing team requires resubmitting the modified permission set for license regeneration any time a grant is added or removed, since the license key is tied to the exact set of grants at the time it was generated.