Can the auto mate flipping be turned of, 9 times out of 10 it filps the wrong mate.
Even better, can you select the mate you want to flip?
To totally stop auto mate flipping I don't think is possible. To reduce it, make sure you check the box under Assemblies for "Prompt before changing mate alignments on edit". Then if it brings up the prompt to change mates for you, just say NO! I haven't had the time to test the option to not ask me again - I am afraid that it will then just not ask and make the changes rather than never ask and never make the changes. And can you select what to flip? Nope. I have tried letting it decide on cases where I knew the one mate that was causing the problem and it flipped about 15 others instead, and moved some parts that were previously fully defined and happy.
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