Aw shucks, ATM! got all serious and dramatic on us and…well, having Tenchi and Momo separate after finally meeting up in the same timeline works about as well as you expect in a four-minute episode. There’s just not enough time for the impact to really land.
Due magical objects like the lightsabers and the cloud of petals, everything is fixed about as quickly as it broke, eliciting not much more than a shrug. Momo and Tenchi return, with Momo back to her original young age. Hugs for all, etc.
It always seemed like she was a deal younger than the other high school girls anyway, and now it makes sense why they protected her so; her mind really was younger. With the return of Tenchi and Lil’ Momo, the rift engulfing Earth vanishes and everything pretty much goes back to normal.