So if you can't load your save since the mod updated:
MainMenu>Load>SelectGameSave>More...>ChooseMods HERE is where you want to re-enable the mods. Just choose spawn-point enabled OR spawn-point disabled. There might also be a CLEAN variant of the shelter, so you might have to choose between CLEAN spawn-point enabled, CLEAN spawn-point disabled, spawn-point enabled OR spawn-point disabled.
Thanks to Sven for helping me figure it out.

The update really messed these shelters up. Now, I can only get them to show up if I select them as a spawn location; if I don't, they just don't exist in the game. Another problem is if I select a shelter as a spawn point, it can't be claimed as a safehouse because it's a spawnpoint... What a headache. It really stinks because these are some great mods. Please revert the changes, or fix it so they're actually usable.

Can somebody help please the shelters won't spawn for me. I have it last in my load order and I don't know what breaks it. I'm running 10 years later but they should work please help!

not a safehouse mean zombie respawn ?

Can confirm, you can't claim them as a safehouse.

cause they are bunkers not houses lol or do you mean you cant Claim them as a safehouse?

great mods, any reason they are not designated as residential?