Did you edit the mod and add the modular NwNCQ haks to the module before removing the original haks from your hak folder?
Sounds to me like this may be the problem. To start with I would add the original haks back into your hak folder then see if the module will open again in the toolset.
If that works the next step would be to add the Modular haks to the module above the original haks, run a build, then remove the originals, run a build again.
saying that, I'm not even sure that will work, don't know if the modular tilesets carry the same naming conventions as the original.