[Spoon]

This had me completely puzzled yesterday. A ship that was appearing (present at the start of the mission) just fine at first, suddenly vanished without a trace in mission. While it was still present in FRED. The only thing I could think of that I changed was its name. I could not make it reappear no matter what I tried. It simply would no longer show up in mission.
Today I started an other mission, changed the names of a few fighters... and lo and behold, 3 of them no longer showed up in mission.
FRED gives no warnings when this happens, debug remains silent as well. Using 5636 SSE2

Thing is, I can't reliably reproduce it. Either it has some mysterious conditions or it just happens at random.

[FUBAR-BDHR]

Can you attach the broken mission? 

What type of name change was it?  I recently discovered a bug in leaving the name the same but changing the case.  Example ShipName to Shipname.  Other then that I change names all the time without issue. 

[Spoon]

Can't attached the missions because 1. it uses custom models 2. I currently don't have a mission file with the bug present, I 'fixed' it by deleting the broken ships and replacing them with new ones. Should it happen again i'll be sure to save it.

A normal name change.