Please note I have read MCPE-144208 and this is not a duplicate, that is a different issue.  MCPE-144208 is an issue with items disappearing after force closing the game.  This issue is regarding mobs including villagers and even name-tagged mobs and villagers disappearing after a nether trip, and the game is Saved and Closed properly.

In one of our villages, all 7 villagers (some name-tagged) used for a gold and XP farm disappeared after a trip to the nether.  All were secure behind iron doors, no chance of lightning as we have rods and no evidence they turned in to Witches. 

We then travelled to our main village and ALL the sheep in the pen and ALL the fish in the aquarium and most of the 30 or so villagers also had disappeared. Some of the Pandas had also disappeared but not all.

We take backups and can see in a previous copy that it didn't happen all at once as in one of the backups we can see we have 2 villagers still in existence in the small village of 7 and the rest are missing. 

This is quite a large world (approx 366MB). We play in 2 player split screen mode. 

We have the copies of the game before the glitch, during (only 2 villagers left) and after when all villagers in the small world disappeared. I also have access to Realms if copies needed.