The NACHA rules specifically provide that these converted checks remain subject to stop payment rules up to the time of final posting, just as if they were checks. (They are not, for example, subject to Reg. E's 3-day advance notice requirement for pre-authorized debits.)
We have run into the same question, and we believe it advisable to place a stop on both entry points (MICR and ACH) for any check that was mailed to a billing creditor.
It's desirable, IMHO, that vendors step up to the plate and provide single-stop capability that will cover both MICR items and converted checks. Until then, though, we'll have to put double stops in place.
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John S. Burnett
BankersOnline.com
Fighting for Compliance since 1976
Bankers' Threads User #8