So my situation is as follows. I work out of state for a major pipeline contractor. I signed a contract that states that the hotels I stay in (i would say live in 8months if the year), since they are paid for by the company, are considered company property. I also travel in a company provided car. Being as I am a couple thousand miles from my home and on my own I carry a firearm in a locked case, inside of my locked suitcase. I travel with my boss.

Recently, I inadvertently got my boss into a lot of trouble for refusing to cover up a major problem he caused and he is taking it personally. He also knows that I travel with a firearm, though he's never personally seen it. He has seen my non descript locked pelican case, however.

I am concerned that he will try to use this as leverage to fire me. My question is how far can a company take a search? I figure they have legal ground to search my suitcases when they are in the company car or maybe even in the hotel room.  Do you think they can legally force me to open the locked case? I was planning on shipping it home ASAP to try to stay one step ahead of this but I just learned that my boss's boss is on the way to see us and write my boss up. If my boss is as petty as I think he is he may use this opportunity to report me.

Local ffl or gunsmith? Might need to be dropped off for "cleaning"?

Maybe they are coming to shit can your boss. If they aren't you should do your best to follow company policy until the heat dies down.

If you think he is going to hold a personal grudge against you it may be best to ask for a transfer.

Because believe it or not finding legit reasons to terminate an employee is not that difficult.

So cover you ass and follow the rules.,

What state? In some of states it is legal to keep a weapon in a locked car on company property.

Your Boss will need a reference for his next job unless he wants to burn that bridge too or his mistake was so negligent that you wouldn't feel comfortable giving it.
I don't see him throwing you under the bus too. To be safe trade the pelican case for a tool box or Tennis racket bag.

That would come as a surprise to the hotel management.

The part in red above is accurate.  Some states provide employees with protections when it comes to firearms.  The traveling can complicate things, but generally you'd look to where you were hired and any sort of home office if you have one.

Rent a a storage unit for the gun or something.. Lock something funny in the case.

That's plan "A" but do to the hours I work I have yet to be able to sneak off to do that.

The irony is that is exactly what got me into this position.

Find a kitchen-table guy who is willing to meet up outside of your working / business hours.  Even if he has to ship the gun back to your local FFL for transfer back to you, that's still better than losing your job b/c of the policy if your boss decides to rat you out.

You can find a complete list of FFL's nationwide at https://www.atf.gov/firearms/listing-federal-firearms-licensees-ffls-2017 and their phone numbers are on the far right side of each line of text.  Start making calls ASAP.

So what happened?

This. I'd fill it with toiletries.  You can also see if the hotel has a safe you can use.