So I let another couple base attacks occur in the next couple months, as I was having quite a lot of fun crushing ethereals. Now, I'm up to 27 Fusion Bombs, 5 more than I had before the last base defense.
It turns out that however many Fusion bombs I have left in the tank AFTER the mission concludes get added to the previous total I had prior to the base invasion.
So I start with 22 bombs + 9 in the Hovertank/Launcher. I fire 4 during the course of the base defense mission and end up with 27 after I win!

I don't know if this is repeatable across games, but I do have an earlier game I played on beginner difficulty that I could test. The game I'm currently playing is on Veteran, though I don't see how that would affect this particular issue. I realize most people here probably play the pc version, but has anyone experienced this particular bug in their games?
Also, apologies if this is old news, but I didn't see anything about this anywhere..