FYSA - I relayed this info to kryojenik via Discord PMs but here's some info for Schuby and for anyone else lurking:
Okay so we have some interesting new behavior and test results
So I'll refer to myself as "I/me" and the other person I'm testing with as "Player 2"
I did the initial migration of the map to Miniloaders modernized.
When I host, Player 2 gets the "migrate" popup and can't dismiss it
We did a test: We had Player 2 load a pre-migrate save and do the migration himself
As a result, he no longer gets the migrate popup but now I do (on the new test forked map)
So it appears that the symptom is that, in multiplayer, the person who DID NOT do the migration can't dismiss the popup
...and:
We've verified this test in both directions:
One of us checks the box
Loads the pre migrate save
Does the migration
Saves and quits
Unchecks the box
Loads the game fine with no issue
The other person, box unchecked, joins multiplayer via steam and gets the migrate checkbox, and clicking "Migrate" does nothing
...
Incidentally: You can just drag the window to the corner of the screen as a workaround to keep playing in the interim. That's what my other player has been doing.