Hi Michael,
This one almost had me baffled, but I managed to get it to reproduce.
The file attached is at step 4. before the fillet, when you fillet this edge the cylinder vanishes.
The procedure was:
1. Offset surface 3mm


2. Extrude cylinder from circle.


3. boolean diff surface from cylinder


4.Fillet this edge 1mm


5. Hey presto! vanishing cylinder


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