An update on this issue. After the incident, thankfully there were some leftover villagers (probably they were babies before the nuke so they weren't deleted, not sure). I was given a suggestion to have less than 25 entities, or in this case, villagers, on each plot to avoid such an issue next time. I understood that the lesser entities the plot has, the less chance they'd be deleted by "clearlag". I kept the precautions in mind; I made a new breeder, made sure to allocate villagers into different plots/chunks.
And alas, it happened again: (Imgur). I really don't know what's going on, but this is definitely ruining my (and others') experience and flushing hours of work down the drain. In this case, there are not even that many villagers to begin with, which made me even more confused.
I sincerely apologize for the passive-aggressive tone, but I'm most definitely not letting myself, and others, to experience such disappointment countless times. I really just need a substantial answer or a rational solution to the case. Because at this point, I might just give up on the game entirely.