I’m still not completely sure what Im looking at.
If you are in fact ZRemeshing the resulting merged UMesh from your boolean operation, it should look something like this at your settings:

Based on the information I have, I can only assume your mesh is faulty in some way.
Also be aware that ZRemesher is not effective with extremely low polycounts. There is no way you’ll get a “half” result from a mesh that is already that low poly to begin with. It should not have produced the result you’re showing here, however.
I recommend subdividing your mesh to smooth it, unless you want that low poly faceted look. Then run your mesh through Dynamesh to clean it up, close any gaps, and eliminate overlapped geometry. ZRemesh the resulting, higher resolution mesh.
If you still can’t sort out the issue with your mesh and are willing, save out a TOOL file–not a project file–with Tool>Save As for the merged UMesh in the new iMage3D format, and drag and drop the resulting image file directly in the text window in the thread here. Save only the subtool required to reproduce the issue, and nothing else. I’ll take a look at it.