Just tried adding Noble Skyrim and regenerating the LOD with Alpha-64, and bang: the tower was gone again. The combination of Fortified Whiterun, Noble Skyrim textures, and DynDOLOD 3 Alpha-64 does seem to be what triggers it. `prid 1000AA28` and disable/enable and recycleactor resulted in no change.
Curious to hear if you're able to reproduce when you add Noble Skyrim to the mix; if not, something very strange is happening on my end, and I'll stop bugging you about this. If you do see this issue, please try walking into the tower area; you should also find that the tower's collision is gone as well as the visual model.
For now, I'm off to bed--it's 4am and I have work in a few hours. Thanks for looking into this!
EDIT: As I went to log off, it occurred to me: if the Noble Skyrim's textures trigger this, is it possible that the relevant change between Alpha-58 and Alpha-64 was in TexGen rather than DynDoLOD? I don't understand enough about their inner workings to know if that's plausible, but I'll try using old TexGen/new DynDOLOD and new TexGen/old DynDOLOD tomorrow when I have a chance.