The sentence that explains why certified checks became rare. UCC 3-409(d) ends: "The drawee of a check has no obligation to certify the check, and refusal to certify is not dishonor of the check." Both halves matter. A bank asked to certify may simply decline, and the customer has no remedy for the refusal, because a refusal to certify is not treated as a dishonor of the instrument. A bank asked instead to issue a cashier's check is being asked to sell its own product, which is a transaction it controls end to end. Given the choice between taking on an obligation on a customer's paper and issuing its own instrument, most institutions steer to the second, and a customer who asks for certification today is often offered a cashier's check instead. That is a consequence of the rule rather than an accident of banking fashion.
The stale-check rule does not reach a certified check, and the carve-out is express. Under UCC 4-404, "a bank is under no obligation to a customer having a checking account to pay a check, other than a certified check, which is presented more than six months after its date, but it may charge its customer's account for a payment made thereafter in good faith." Read the three words in the middle. The familiar six-month rule, the one that makes an old check awkward to deposit, carves out the certified check by name. The reason follows from the structure: the bank's refusal option in 4-404 is a right against its customer's order, and on a certified check the bank has already accepted and taken on its own obligation, so there is no order left to decline.
What does run out is the time to sue on it. UCC 3-118(d) provides that an action to enforce the obligation of the acceptor of a certified check, or the issuer of a teller's check, cashier's check or traveler's check, "must be commenced within three years after demand for payment is made to the acceptor or issuer, as the case may be." Subsection (f) confirms the point from the other direction by excluding a certified check from the six-year rule it applies to other accepted drafts. So the clock starts at demand rather than at the date on the instrument. A certified check found in a drawer years later has not aged out by its own date, and the holder who presents it and is refused has three years from that demand to act. Separately, funds left unclaimed long enough become subject to a state's unclaimed property regime, which is a different mechanism from either rule.
What certification actually does to the money, precisely. UCC 3-409 says nothing about setting funds aside; it defines acceptance as the drawee's signed agreement to pay. The set-aside idea comes from banking regulation, and it is conditional rather than universal. Regulation CC's own definition at 12 CFR 229.2(j) says a certified check is one on which the drawee bank certifies either that "the signature of the drawer on the check is genuine" and that "the bank has set aside funds" equal to the amount and to be used to pay the check, or, in the alternative, that "the bank will pay the check upon presentment." So a certified check may qualify without any earmarked funds behind it. What the payee is relying on in every case is not a segregated balance but the bank's own accepted obligation on the instrument, which does not depend on what the customer's account holds afterwards.
Deposit and availability, in one line. Regulation CC gives a cashier's, certified or teller's check next-business-day availability only where it is deposited into an account held by a payee of the check, in person to an employee of the depositary bank, and with a special deposit slip or envelope if the bank requires one (12 CFR 229.10(c)(1)(v) and (c)(3)); where the deposit is not made in person, 229.10(c)(2) gives the bank until the second business day. The mobile deposit page covers that condition and the four instruments it reaches.