Im working on an iron farm right now in the beta so I have a villager breed linked up to a nether portal, but some of the babies when they go in are not there. I'm pretty sure it happens if you don't follow them through the portal right away. Whenever I try to AFK the farm, most of the villagers are not in there. It is really annoying because I've lost probably 15+ villagers from this. All my portals are linked up properly.
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Thank you for your report!
We're actually already tracking this issue at MCPE-66818, so I will resolve and link this ticket as a duplicate.
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Similar kind of thing here. Because of Bug MCPE-69757 (reported by me) in that existing villagers dont offer more trading before lockout, I am using a breeder to replace existing villagers with new villagers that do follow the new trading mechanics. I use the Nether to transport the new villagers but in doing so existing villagers at my base are despawning at random. Sometimes you lose none, but you can lose between 1-3 villagers on some visits to and from the Nether. Trying to find a pattern/trend but non so far except only the villagers on one side of the trading hall are despawning. The other side of the hall is unaffected as yet (they face each other)...