I would put it on inspection in the controller, jump that intermediate lock circuit to verify its the intermediate locks. REMOVE the jumper then put on just hoistway door bypass, not car door bypass. Then go get on top on inspection and run the shaft to find your problem. Find out which order they wired the intermediate locks in, in other words if 2 doesn't have power, does 3 or 1? If 3 doesn't go up to 4. Etc. Depending on if the controller backfeeds both sides of the intermediate lock circuit when it's on hoistway bypass, you may need a helper you can put in the machine room so you can run to each lock on the cartop, then radio him to take it off bypass so you can check things, then put it back on so you can run to the next floor.
Most likely since it's your intermediate locks worst case you'll have to pull a new wire between 2 floors. Or it could just be a lock/contact.