I can think of one in-game effect than MIGHT explain it, but if that's the case it's exciting, as I didn't think it would work that way.
If the embark world tile or the world tile "providing" the biome for the embark is under the influence of a site spreading evil that also spreads death, all the trees and all the vegetation in that biome will be dead (doesn't count subsurface trees/vegetation, and I'm not sure if surface farming works, but guess it would).
If something kills off the source of the spread of evil, the area affected can contract (it somehow doesn't seem to happen in all instances even though it ought to, but it does sometimes, at least). I didn't think such a contraction (or, for that matter, spread) would affect an active fortress, but if it does it ought to have the effect that things start to grow again.
Using DFHack you ought to be able to change the Evilness value of the world tile controlling the biome (embark world tile or a neighbor) to be below the threshold of Evil. This definitely ought to work pre embark, but if spread and contraction affects active fortresses it ought to work even on an existing fortress (I'd hack the value, save and reload, using a copy of the backup to allow you to revert to your original backup). Also note that if the "new" game doesn't have the evil dethroned as it was in the original game, evil may sweep over the embark again as the Evilness value has increased back over the Evil threshold (all of this assuming this is what's happened to the game).
If you do try it, and it works (and it wouldn't hurt with a report if it fails as well), please report back, as this is something that hasn't been researched much, as far as I know.