the workflow works IF there is a slight difference in the overlapping. for example like this:
the issue is that when you do it with the perfect connection, the remining faces after the partition will be exactly the same in the two sides, so the glue face tool will remove one.
with the modified geometry it works like charm. If you want to still use the perfectly aligned you need to use the second option of the glue face tool where you can select the faces you want to glue exactly and not glue everything you can version.
here is a .hdf example (with slight modification of the face):
exampleGlueFaces.hdf (193,4 KB)