I would first make sure that the geometry for the groin vault makes a solid group/component. Then I would place a cylinder where I wasn the hole making sure it is also a solid object. Then use Subtract from the native Solid Tools or from Eneroth Solid Tools to cut the hole.
Inorder for the groin vault to be considered solid, every edge must be shared by exactly two faces. No more and no fewer.
By the way, I noticed incorrect tag usage in your model. You should be keeping Untagged as active at all times. Create and leave all edges and faces untagged. Only groups and components should be given tags.
The Tags panel when I opened the file.
The result of removing tags from the edges and faces in the model:
It’s also a good idea to purge unused stuff from the model once in awhle.
