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It's never too late to keep a thread going, huh? <g>
The Flatten/Components/Redefine/Orient (uncheck AlgnToSeg) does not fix the misalignment problem I was decribing. The Orient command is a way to make a datum or face on the Component (i.e. the connector) parallel to a chosen datum on the flattened harness. Yes, that will make the Component "square" to the harness leg, but the connector will still be off-center.
By "off-center", I don't mean "angularly misaligned". I mean that the centerline of the harnessleg does not meet the connector at the physical midpoint of the connector. The centerlines of the harness leg and the connector are parallel, but offset by some distance.
PTC support did not have an answer for this behavior.
It's a Wish List item, I suppose, but it'd be nice if connectors (Components) would line-up nicely with a leg of a flattened harness just like an attached backshell does: centerline-on-centerline without an offset.
CAD development is like baseball. "There's always next year."
Keep it alive part 2:
With a circular connector containing a single entry port on one end and a non-circular connector on the other end that has 2 entry ports, the behavior seems to align the single entry port csys with one of the other csys, and the Redefine component command will not override this alignment even if you have 2 center planes on the connector. The failure is that one of the 2 wires will not fan out due to insufficient length even when the routes are Free Length. PTC now has now live support for cabling so I'm still waiting. This does not reflect well on PTC.