Related to MCPE-52460

To sum it up, villagers are despawning. After dealing with them several times I can only guess it's a couple of things. Their coordinates when they change animation aren't being confirmed causing them to vanish entirely when their animations are changed back to default standing.

Villagers will despawn/become transparent/cease to load during very common circumstances.

1. Going to bed.
2. If it's night and you are fighting enemies near them, they might vanish even if in beds or confined.
3. Leaving the block and coming back.
4. Simply saving and quitting and returning.

Basically as much as I can tell there is no check being done to make sure they are placed back in the world during any event that changes their animation from standing to laying, or invisible to standing.  [If the chunk they are on is unloaded.] The villagers have returned once out of all the times I've dealt with them and that because I bred new villagers to take their place.

The thing is is I also believe the mechanic designed to have them be 'targeted' by monsters once you meet them is also causing them to despawn. Rather than the monsters spawning more around said town, or in dark places inside said town, once designated as targets the villagers are just vanishing in general. 

Many players have had this issue and I can only believe that the mechanic designed to have a village targeted is the common denominator in all people's issues. I also did trap villagers when I noticed that only 4 out of 10 were remaining. When I got a healthy pool of villagers, if one vanished, all the ones in nearby coordinates also vanished. Aka I trapped all of them, most of them were spawned and bred in town, the ones that reappeared, vanished again along with all the ones that I spawned.

I checked underground and blocks around the area which I kept them and they weren't there... [And it also led me to die on hardcore mode...]

Other Villager related issues.

      1. Beds near walls can sometimes cause villagers to spawn on the opposite side, same with people.

Other despawn related issues.

      1. If you dismount a moving boat, it can vanish underneath you, and force you to reload in order for it to return. This sometimes worked with checks on villagers.

      2. If you dismount a horse in water it also has a chance to vanish entirely forcing you to reload.

      3. A horse in general even if you put it in a safe place, if it has a saddle it has a chance of becoming invisible, forcing you to reload the game to even see it again.

      4. Despite villagers/farmers being absent, some areas will regrow wheat which requires seeds and someone to plant them. 

 Other performance related issues.

      1. The game even in solo player mode is experiencing hiccups where enemies jump forward in time. This can cause a player to either get hit repeatedly or to cause their strikes to miss even when the target is in the correct area. It can also cause very awkward lag in character dense areas.