Hi @cmaciel,
Welcome to the Auth0 Community!
I understand that you have not been able to set the user_metadata for Passwordless Users in a Pre-User Registration Flow.
After testing this myself, I noticed the same observations as you where updating the user_metadata does not persist in the user profile. More interestingly, when using the Realtime Webtask Logs extension to print the event.user property, the user_metadata shows the updated values but ignores updating them in the user profile.
Moreover, after checking with our Engineering teams, I can confirm that this is a known bug and has been moved into our product backlog to be addressed. However, I am unable to provide an ETA as to when this will be fixed.
I hope this answers your questions.
Please reach out if you have additional questions.
Thank you.