we recently merged few vendors and one of my subsidiary doesn't do ACH an one does, so when the subsidiary that does check run, cannot pay the vendor that has ACH information because NetSuite thinks this vendor is paid by ACH, so as a workaround they have to uncheck those vendor payments and do each payment individually which can be time consuming and erroneous. any one ran into this? or have any solution?

I'd be tempted to unmerge the vendors.

Can you unmerge? It said it's irreversible process when I merged

Oh by un-merge - I mean create new, separate vendors and then migrate the appropriate transactions.