Culling means a sim will be deleted in order to make more data space for the game to function well. I've never experienced any living sims to be culled, maybe MCCC stopped it...I'm not sure. But I know when you get the notification that a sim's spirit is fading away, it's a warning that a ghost sim is going to be culled. This usually happened when you haven't interacted with that sim after one became a ghost. Ghosts are in hidden households, unless modded, you can't find them in the manage household.
As for OP's mysterious townie boyfriend, are you sure you look through every household? Did you look into the "Not in the world" category? Usually, the townies that game spawns can be found there. But if you enable the "fill the empty house" in the game option, or you have mods which allow homeless to move in, it's a highly chance that the mysterious boyfriend had already moved in.
As far as I know, sims will disappear from the game once culled, just like they never exist! You can't find them in the relationship category, either. Logically speaking, they can't call you or send texts since they no longer exist. If you can't find a sim in any household, and this sim still show up or contact with you, which leads to the only explanation: this sim has already be in the hidden household. There are some NPC in the hidden one such as Senior Pollination Technician #3 and CurioShop Owner. I think maybe the sim you're referring to could be somehow being in hidden household.
If you really want to play that sim, you can use cheat to add him to your household. Click ctrl+shift+c at the same time then your see a blink pop up, then type "testingcheats true", once it's done, holding shift and click the sim that you want to add, you'll see the option "add to family", click it then the sim will be in your household right away. And be careful! A sim you add will lose their NPC job like gym trainer, DJ...etc. You can also use the same way to remove a sim from family, which will make one become NPC, and the one you remove by cheat will be in the hidden household.
Another infamous culling is baby, toddler or child being whisked away. Sending alien baby back to homeland is also counted as culling. Once happening, they'll show up in a hidden household without any data. I wasn't sure about this one, but I once sent an alien female baby back, then I used MCCC to see what was really going on, it turned out that the baby was in a hidden household which I could only see it with MCCC, and MCCC informed me of that it couldn't find any data about that baby. But MCCC still stated that my sim had a daughter. and I checked the genealogy, the baby was still showing there. So I guess culling the babies, toddlers and children in this way will delete the date of the targeted sims, but the relationship will still remain.