This bug has been fixed in the latest update,sorry

I've had the same problem more recently, seems to still be an issue.

Does happen sometimes.
When characters are loaded onto craft, game acts as if they don't exist anymore.
Some side effects include loss of automatically assigned Ideology roles (like best crafter leader) and regain of them once that pawn is released, and such.

When all pawns are loaded on a temporary map, that normally will disappear once caravan leaves it, it may disappear together with the craft before it actually leaves, erasing the craft and all contents including pawns.

It also can just vanish when sent to an event tile, probably for the same reason - it arrives, game creates the map, thinks there are no pawns and immediately deletes the map together with still flying craft

Happened today to me as well. Landing on a quest tile and unloading my pawns on the map had no issues at all. But when i had to load everything and everyone again, i started having some issues.
It seems that manually telling someone to get on the aerocraft (without using the "set to load" button) just makes pawns disappear.
Also pawns that refuse to do dumb labor (such as the "Transport" job, which designates which pawns load things onto caravans) just refuse to get on, even when i use the "set to load" menu. Thankfully i was able to circumvent this with another mod that lets me force pawns to do jobs they would otherwise refuse to do, at a cost of a heavy mood debuff.

Another thing i've noticed is that if a pawn were to get off the aerocraft after being loaded (because they need to eat, for example) they just disappear from the load menu afterwards, and since manually loading pawns makes them disappear in tiles that aren't my own colony, it means they just cannot return home.

After some trial and error, i managed to get everyone home. But i had to wait until my pawns manually loaded everything onto the aerocraft, as opposed to everything loading instantly like a regular caravan.

Other than that, i haven't had any other issues with combat and all that.
Keep up the great work on the mod!

I used the plane to clear one of the VE mechanoids frigate, but as soon the frigate was destroyed the map closed and the plane (with the crew) vanished, like when you lose a caravan.

Originally posted by Genebra_Chan:

I used the plane to clear one of the VE mechanoids frigate, but as soon the frigate was destroyed the map closed and the plane (with the crew) vanished, like when you lose a caravan.

^ This

This is exactly why I came here. I am having the same issue. The pawn card vanishes and the game acts as if the pawn is simply gone while inside of the ship, and upon clearing the VEFM ship, the map closes and the pawn/plane are gone.

this bug still exists, i have to keep using the debug menu to create or instantly move a pawn from my base to where i want to use my aircraft otherwise i lose them.