It's really hard at this point to know what's happening with the joeys. There could be many reasons one of the joeys are missing.
So I'll give you a brief class on glider gestation to make sure you understand how this process works.
Once the embryo travels to the pouch it latches on to Mom's nipple. Their jaws lock at this point. If they ever let go or are pulled, they can't relatch.
Many things can happen to the Joey at this point.
Joeys have to be cleaned of excrement while they are attached many times a day. That's mom's job. One could have been accidentally pulled off during this process.
A Joey may have had issues and was deformed. Nature takes it's course.
A new mom may have been over cleaning in her pouch.
There are several other reasons as well. Age,Jealousy, diet
, stress and choice.
It's normal for them to "clean up" after a Joey dies to keep the smell from attracting predators. Since they are still exotic and not domesticated, Instinct kicks in.
It's heart breaking sometimes. The only way to keep this from happening is to neuter the male. There may be "surprises" after that's done.
Please keep us posted and please don't feel bad. I'm not sure I explained it well, so please ask more questions.