In my last play through, I locked up a target in HAD and forgot about it. I switched to AA master mode and noticed that MASK popup on HUD (from my TGP pod still area stabilized somewhere).
While still in AA mode I manually toggled the HAD and TGP pod’s power both off on console. For some reason I couldn’t lock or “bug” any air targets. Luckily I was fencing out. It came to me to just reverse my “actions” in the cockpit and found out that when I briefly went back in to AG master mode and toggled my HAD and TGP pods back on (don’t remember if I changed HAD targets or not) I was only then able to go back into AA master mode and select air targets as usual. Don’t really know what caused issues or what solved things, but it happened.
I haven’t tried to recreate the problem. Don’t know if this helps OP in anyway either.