Again - the altertables shouldn't be run more than once.
I would restore to before you ran them and run them again - in order - only once.
If the altertable gets run more than once - or gets interrupted - all the private messages end up assigned to User Number 0 - so they are gone - or there's no way to piece them back together - other than restoring and running the altertable again uninterrupted.
The upgrade instructions suggest dumping old Private Messages (from the admin menu) before the upgrade - as that step is intense - and depending on how the server is setup it can time out.
[]Before upgrading you may want to purge very old private messages via the admin section. This upgrade makes some major changes to the database structure and the step to process private messages can take the longest.
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