I just went through one of the missions (minor spoiler):
the Honey Bee missile mission
and it glitched out on me, so I had to abort the mission and restart it. As I went through it again, I saw that resources I found in my previous run were still marked on the map, and were now marked as "Obtained". On the other hand, all the bases/enemies respawned as expected.
Did I get to keep the resources I acquired in the aborted run?
Did I get to keep the soldiers?
Unfortunately I can't tell myself from looking through my mother base info, so I'm hoping someone can confirm whether you get to keep these things if you abort a mission.