I had two subfleets of Battle Fleet called "1st Fleet" and "Home Fleet". Home Fleet had three subfleets of four ships. I Detatched Home Fleet, and it showed up as an empty fleet, and there was no way to find the ships that were supposed to be in it - the class window showed them still existing, but they didn't show up anywhere. I reloaded, set up a subfleet with subfleets, and detatched the first level fleet again. Exact same result - detatching a subfleet that has subfleets removes all subfleets and casts the ships in them into Limbo.
Reproduced and fixed.
I had a similar bug today, its different enough I figured I'd mention it in case your fix doesn't also cover it.
Issue: using the 'divide into single ships' order with a detached sub-fleet made out of ships landed in a mothership causes said ships to be eaten by the space kraken and disappear. This has a follow on effect of making it impossible to assign ships to said carrier. Restarting the game allows new ships to be assigned. Choosing to detach a single ship into a fleet, then adding other docked ships to it and using the 'divide into single ships' order has a similar effect, with the difference being that the originally detached ship doesn't get deleted.
Combining the carrier with a different fleet causes the deleted ships to reappear (highlighted to provide people who encounter this issue a workaround). This issue occurs with both fighters and FACs. This issue appears to be related to ships being docked in a mothership.
How to reproduce:
1) Create ship with hanger space, assign and land ships in it using the 'land on specified mothership + assign' order. Advance time 5 seconds. Create a subfleet within the carrier's fleet and move docked ships into the subfleet. Detach said subfleet and order it to 'divide into single ships' in the same place as the carrier (tested locations: population, jump point, and the carrier's fleet). Advance time 5 seconds. The detached subfleet will have disappear from the Naval Organisation window with no error produced.
2) Order additional ships to land onto the carrier using the 'land on specified mothership' command (+assign and don't assign has no impact on this step). Advance time 5 seconds. The ships ordered to land will have remained in their own fleet and won't have been assigned. No error message is produced.
3a) Combine carrier with new fleet. Deleted ships should reappear; 3b) Save and exit the game. Restart. Order ships to land onto the problematic carrier. New ships will land with no problem.
Some other issues I found testing this: [major] ships equipped with commercial hangers apparently cannot be selected using the 'land on specified mothership' order (both functions) and thus cannot be used at all, [minor] commercial hanger deck isn't included in the 'Hanger Deck' category in the ship design menu and instead sits underneath the 'command and control' category - is this WAI?