After I do the Companions main quest to kill the Silver Hand guys, Valtheim Towers stopped respawning. I've waited more than 30 days in Breezehome to force cell reset, but there's nothing. The reset solved my other problem with Eldersblood Peak, so I know the reset succeeded.

What is happening here?

What version of skyrim are you using..? This was fixed way back in 1.6.

But what's happening is, there was a bug where if you visited cells prior before they reset, it stops the respawn timer indefinitely. This can eventually empty your game and turn it into a wasteland.

Valtheim Towers was the go to example for many, including myself that reported it because after about 3-4 visits it's not hard to notice they aren't spawning anymore. Soon you will notice all the dragon lairs being affected by this as you visit them. Forts, etc.

Before the patch, there was no known fix.