Converted checks do come under the ACH rules, and those converted to ARC, POP or BOC Entries are also subject to Reg E when they affect a consumer account. RCK (Re-presented check) Entries remain subject to UCC rules and ACH, but not to Reg E.
As for the stop payments, in many cases your customer won't know for sure whether a check conversion has taken place. That is one reason that extended return deadlines apply to ARC, BOC, POP and RCK Entries.
Frankly, if a stop has been accepted on the original paper check, there is no authority to pay the derivative ACH entry.
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John S. Burnett
BankersOnline.com
Fighting for Compliance since 1976
Bankers' Threads User #8