The problem was two fold:
- REPAIR TABLE t1 USE_FRM did not work for transactional
  Aria tables (Table was thought to be repaired, which it was not) which
  caused issues in later usage of the table.
- When swapping tmp_data file to data file, sort_info files where not
  updated. This caused problems if there was several unique keys and
  there was a duplicate for the second key.