Why do they have per diem rules? Storage. Many companies actually eat the per diem costs to avoid having to build a storage facility. Plastic pellets and propane are two commodities commonly used with storage cars.
Per Diem charges are paid railroad to railroad, while Demurrage is paid by a customer to railroad. Currently there's a big stink rising between customers and railroads on demurrage charges with a combination of rising rates and inaccurate invoicing. Auditing demurrage is a time-consuming nightmare (I've done it - blah ) and reconciliation can take months with the clock running on incoming cars all the while. Another factor in the demurrage mix is bad order empty boxcars, delivered to an industry for loading, but with trash inside or mechanical defects. These are thought to be suitable by the railroad, but not the shipper and calls have to me made to change the car status. Meanwhile loads sit on the dock awaiting good equipment …..
Yep, that's a serious infraction. So is mistakenly returning "empty" tank cars with remaining hazmat quantity inside. The cars move on Bills-Of-Lading and with placards showing as empties, yet with a reportable quantity inside, could create a startling and dangerous situation if in a derailment or if a leak occurs.
Car hire ( the modern term for per diem) is calculated on a combination of hourly and mileage charges. Private owner cars tend to be on a mileage charge not an hourly charge. Railroad owned cars tend to be on an hourly charge. Per diem was originally assessed because railroad in the 1800's would just keep foreign line cars (railroads employed "car tracers" who tracked down "lost" cars). To discourage that and encourage railroads to build their own cars for their own business they railroads started charging for a car's use. Demurrage is the charge that discourages using cars for storage. Demurrage also may not apply to a private car on private track. Back to the original question, the railroad crew would pull all the cars they were told to pull. If their paperwork says to pull the car they will, if the paperwork doesn't say to pull the car they won't.
The bill of lading is the document/communication the shipper has with the railroad, the document that the railroad uses to move the car on the railroad is the waybill. They have similar information, but are different documents.