Can't Split two Objects

Hi - I need to produce a triangulated surface description from solids in a step-file. Often there are shared and touching surfaces.
I have been using MakeConnected extensively to handle such surfaces, and also tried using Splitter. However I have found cases where this results in faces being excluded instead.

One such situation is shown in pic 1. It is basically a can with a pipe-through a hole in the side-wall of the can. For my application I need the edge nodes of the pipe to coincide with the ones of the hole in the can. As mentioned - for other geometries - things work fine but not for this case.
After triangulating it looks something like pic 2 which is a closeup of where the pipe connects to the can.
I.e. after I have triangulated both shapes, the pipe has lost one surface. What is the proper way to handle the situation? I would have thought that for instance splitting the pipe with the can would create the necessary boundary edge on the pipe, but that seems not to be the case for some reason.
Any ideas? What can cause this behaviour?

cheers

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