WARNING: the following post may contain spoilers because I don't know how to ask the question without describing the mission elements.

I have been storing all my weapons, gear, items, etc. in the ammo(?) box on the right corner of the main desk in front of you when you walk into the boston police station.

At some point, this facility is attacked (when you get the prydwen) and the structure appears to have changed a bit.

The box is no longer there. Yes, I have a backup save, but I put in many hours since then before I went back to the police station and realized the box was gone.

Is there any way to find this box? Or are my items just gone?

Your items are gone unless you use an earlier save. Don't leave your things anywhere except within settlements (preferably transfer to the workbench) or

I feel you...I lost the Big Boy from Arturo the same way....do this^