To clarify, I encountered this behavior on Custom Map #373 (http://knucklecracker.com/forums/index.php?topic=22469.0), wherein I destroyed a Progenitor, destroying all enemy structures, but leaving enemy lathe ships alive to flip my starting emitters. It is in this map that I have done my testing, the results of which were:
Regardless of how many times the emitters were flipped back and forth (if at all), when I would save and load the game
-If all flip emitters were blue, the game would load with the objective Collect.
-If any emitters were red, the game would load with the objective Destroy.
Assuming that it is intended that the objective should remain on collect, this leads me to suspect that when the game loads, it determines the objective by looking at the map state, as opposed to remembering what it was when the game was saved.
Alternatively, if it is intended that the objective should revert when an emitter is flipped, that for some reason the game isn't checking/updating when a flip emitter is flipped, but only when the objective has already switched to Collect.
Spoiler
However, I am reluctant to admit that might not be the whole story here. I also encountered two anomalies.
Once, the objective switched to Collect despite there still being one red emitter remaining.
Once, the objective being Destroy and all items collected, the map completed despite one red emitter remaining.
At first I suspected this might be due to some of the emitters being flagged as mission goals and some not, but no matter in what combination I lathed them, I was ultimately unable to reproduce this issue at will.
Without knowing how to open the mission in an editor, nor to debug/check logs, I am unsure how to investigate this further.
Additionally, I performed a quick test in the editor to confirm that this behavior was not limited to one map, which it is not.