If the free version as installed and it was loaded by WP before Pro, then you were actually using the free version and not Pro (or some strange combination of the two).
I’m not sure what you can do to correct whatever happened.
This is what I would do, but there’s no way of knowing if it will work.
1) backup the database
2) deactivate ACF Pro
3) activate the free version and see if you’re field groups/fields reappear
if that works, don’t try to edit anything
4) Activate the Pro version and go through the update procedure
