After triggering the first map of Surface Tension, moving back into the last map of Questionable Ethics (so that the shutter door resets) and then moving back in will cause Gordon to go into a permanent “stand down” state (like when he’s pointing at an ally in Half-Life 2), unable to use or switch weapons. Attempting a quicksave and then quickloading after this happens will erase all weapons. The only option is to hope you had an earlier autosave, which I did.
While I was using the latest version of the Surface Tension Uncut mod, I had obviously gotten nowhere near the point where the changes were made, as I was right at the beginning of the chapter.