It’s the same system utilized by Triffids as well, destroying the Heart renders the entire grove and its surronding population defunct in short order. The reason Fungaloids don’t wither and die is because they aren’t as intrinsically connected to the towers/flowers/beds that spawned them as Ants are to the Queen or Triffids to the Heart. Fungaloids are capable of rapidly self replicating in a relatively short amount of time, so long as they remain in the reality bubble. Outside of it in the unloaded world they’re statically held in place and thus no new ones will spawn without fungal structures.
It sucks to lose a base like that I know, especially one you built yourself by hand. But now that you know how everything works and what to do preventively, your alot better prepared to tackle this stuff in the future.
Edit: Plus, this is great role play and story building fodder. You’ve already lost everything to the Cataclysm, now the Fungus has taken all your hardfought progress away again, there won’t be a third time, not while you still draw breath.