I decided to drag and drop rearrange the 'Mechs in my bays. I then went to refit a 'Mech damaged in my most recent fight. When I exited the refit screen my Atlas D II had vanished from my inventory. I reloaded the game, refit the damanged 'Mech without rearranging my 'Mechs in the 'Mech bay, and exited the refit screen and all my 'Mechs were present.

Just a warning to those who might try to do the same and encounter the same bug, and I'm hoping the devs will read this and look into fixing the issue.