Alright this is a tricky one, from the sound of it, it seems like you gave them total control of the operation and your authority which is BAD, never ever do that in any case let alone intermodal, how many containers are we talking about? loaded or empty? How much is per diem for each? how many chassis? most steamship lines give 3-5 days before per diem hits, you will need a trucking company that has interchange agreements with the chassis providers, and with the ship lines that own the containers, no one else is permitted to pull those containers and chassis, now if you get in touch with the EPs ie Equipment providers, and they find out why their equipment was held, they will most likely ban you in IANA/UIIA and void your interchange agreements because you failed to fulfill one of the major key parts of the interchange, so careful and better not tell them, instead if you have a truck go and pull this equipment yourself or have someone do it under your MC and return it, otherwise have a carrier that services the same terminal do it, DO NOT LET SOMEONE WITHOUT IANA/UIIA ATTEMPT TO RETURN IT.
Now back to the issue, looks like you cut them off suddenly without ample notice, in that case nothing they can do, not their fault, they can not move their trucks anymore with your company name on them, they can't be under dispatch or haul a commodity or an empty container, so if this is the case then some of the blame falls on you, you should have instructed them to return the equipment first then cut ties.
I'd say, return equipment first, pay per diem and chassis rental, and move on. not much can be done.
You will likely have to pay all the late fines. But than your lawyer will have to seek the money back from them. It will cost some, let’s just hope they return all the equipment, that’s the best that can happen, will take some weight off your shoulders.
File a police report for each piece of equipment. That will stop all charges. You are paying rent on each chassis daily about $20-25 per day. Detention on the box is about $165 per day and some go to about 300 per day, after so many days. You will still have to pay the charges up to the day you file the police report. Your insurance will have to pay for the equipment, but not the charges. We had an agent one time leave an APL box out (before chassis charges) and it racked up $12,000 in equipment detention. The box wasn't worth $2500. After it when to APL collections dept, I was able to get them to agree to $5000.
Intermodal is not for inexperienced trucking companies. I have seen large LTL and TL carriers take a screwing, because they thought they knew everything about trucking. They quickly said the hell with this stupid ####.