I believe the 250 is stocks per account. Make sure none of your old PM accounts have more than 250 stocks in them which have quantity of 1 or higher (it does not seem to import completely sold stocks so you can probably exclude those from counting the 250).
Also as a precaution, rename all the old accounts on that screen to guarantee they will not try to import into an existing watchlist with the same name (from a previous attempt) that already has stocks in it which could cause you to be going over the 250 limit. You can rename them later if they migrate over. You should try this first if you have not already.
As far as not checking all the accounts, at one time, despite that warning message, you could uncheck all but one and try one at a time and then repeat with the others, but they have made changes to the import process since then so I don't know if that still holds true - the message certainly does not imply such but that was the same message that appeared when one could do it so who knows. Not even sure if it would help with that particular error though.
One thing you could try is use a different Microsoft account, create two accounts in the old PM, if you even still can, with a couple example transactions in each, then test checking off just one of them. If it succeeds, try to do a retry import and see if the other is still there and available for import.