Regarding a dispute of an ACH transaction. Per NACHA rules a merchant has 120 days in which to reply to a chargeback request. Per Regulation E if the bank provides provisional credit of a disputed item, it can extend the investigation period to 90 days for an ACH item. Can a bank keep an investigation open for the 90-day period just in the hopes of getting a response from the merchant during that time period?

Sure, if you are waiting on a merchant response, the investigation is not complete.

Just to clarify a bit, even with provisional credit issued, ACH claims only have 45 days to resolve.

And to put a finer point on it, that 45-day period can be extended to 90 days if the EFT was not initiated in a state (it could be an IAT) or resulted from a point-of-sale debit card transaction (POS entry code), or occurred within 30 days after the first deposit was made to the account.