I’ve been trying to reproduce this error, but currently with no success.
I can think of no reason why Element Report would not be re-generated, except where they were either not in the version being re-generated, or do not have a Profile for the elements in the report.
I’m looking into both of these. They MAY be some cases where, if you edit a document to add a new ER section, but don’t save it, then the re-generate won’t pick up the changes.