Spy bug on flipping planet

I can't say I've experienced that one (yet), but then again for me to see other Civs dropping spys on others is uncommon for the most part at least at "tough" difficulty (TA). Even so, most seem to be nullified after a short number of turns by the other Civ. anyway and as you say if a third party spy just happens to be on a structure for which you have incompatible tech when the flip happens, well that would seem to be a rare event, especially leaving that orhpaned spy... what are the chances of that!

Thanks for your observation. Now I'll be looking for it!

What happens to spies from the mega spy event still present when a planet flips?

I almost never get mega events for some reason. I haven't had mega spies pop up in the past year of playing the game - they used to happen fairly frequently, now I just don't see them.

But for the most part they are the same as normal spies - when the planet flips, the new owner is stuck with them unless they were his to begin with. It's only when the improvement is destroyed that this issue pops up, and I haven't yet seen that with mega spies. Hell, I've only seen it with regular spies once. Given the lack of people popping in and saying "yeah, that happened to me too" I'm guessing the vast majority of players will never see this unless they specifically try for it.

Actually, via the cheat system you should be able to recreate this easily.  Plant a spy on a planet that is about to flip to an opponent, then swap to that opponent's race and save the game.  Make sure the planet will be flipping by making it deep in their influence aura.

In ToA 2.03 (In the Arcean´s Last Stand tournament) I had an inevitable CTD once I destroyed a colony where a spy was placed onto. After 4-5 times I disillusioned nullified him - the colony-destruction then worked, but I could have used that spy somewhere else better.....