Not sure if this is exclusive to APQ stage one or not but summons sometimes disappear when using the in-map teleports. No "time has run out and will disappear" message shows. Below is a video I caught of it happening to my Marksman (Frostprey) but it also happens with my Bishop (Bahamut) so it must not be an issue with a specific summon skill.
Ah I know this one. To the best of my knowledge, it happens in maps with long teleports, which is why you encountered it in APQ and FTP1. If you go through the teleports, the summon can reappear and disappear, and sometimes it will reappear on your screen and function (attack, stun, etc.) but not appear on someone else's screen (it will look like an invisible summon is attacking.) Not sure what the fix/root cause of this issue is. Though, reusing the summon skill or teleport should fix it.