I discovered a bit of a complex issue, not sure exactly what happened or why.
The situation:
1. Main Fleet is named the 1st Expeditionary Fleet. This fleet contains several sub-fleets, including four assault groups and two carrier groups. Three Assault Groups are currently detached from the main fleet
2. I detached the two carrier groups using the "Detach" button.
3. I launched fighters from the 1st carrier group using the "Launch All" button.
4. I detached the six scout fighters from the rest of the fighter group, again using the "Detach" button
5. I split the scout fighters into three two-ship groups, and sent them across the system to scout possible enemy locations.
6. I landed the 1st carrier group's fighters on their carriers using the "Land on Assigned Carriers/mothership" command. At this point only the scout fighters remain in space
7. The scout fighters discover enemy ships, and I detach one carrier from the 1st Carrier Group and launch its fighters using the "Launch All" button. The fighters launch an ultimately unsuccessful attack and head back to their carrier.
8. I launch all fighters from the 2nd Carrier Group to end the problem.
9. At this point I decide to consolidate the fleet and move to a location closer to potential targets. I order the 1st, 2nd, and 3rd Assault Groups to join the 1st Expeditionary Fleet using the "Join as Sub-Fleet" command. I also order the 1st and 2nd Carrier Groups to join the 1st Expeditionary Fleet using the same command.
The problem appears when I hit the five second advance. The five groups join the 1st Expeditionary Fleet as intended, however, approximately half of the 2nd Carrier Group's detached fighter wing simply disappears, as does four of the six scout fighters from the 1st Carrier Group. Their fleets (containers) on the Naval Organization window still exist, but they have no ships within them, or, in the case of the 2nd's fighters, just under half of what should be there. They aren't in their correct fleets, and they aren't on their motherships. They appear to have just disappeared. At the time of disappearance they were approximately a billion kilometers from their carriers.
I was a bit frustrated, as there appeared to be no easy way to fix this. I could add in the missing fighters, but they would be at 0% training, which would be annoying given how much effort i put into getting them trained. Fortunately I found the thread on how Aurora makes backup saves, and restored to a previous save before the incident happened.
Still, annoying and worrying for the future. I suspect that the problem lies within the nested relationships between the fighters and their carriers, and their carriers moving from being independent to becoming a sub-fleet.