Pretty sure it's Rolls-Royce, not Boeing, that's handling the bulk of the re-engining program. They're the ones that won the multi-billion dollar contract for it, not Boeing. Boeing is almost certainly involved, yes, but they aren't the main drivers for this contract.
Besides, I don't think this is even a delay. You have to remember, in order to not reduce the availability of the B-52 fleet they are only doing the engine upgrades when a particular B-52 goes into scheduled depot level maintenance. They are not pulling B-52 out of line service to get new engines even if it means it takes longer to fully upgrade the fleet.