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I don't use the collision detection at all but I would say that you could over-size your pipes and equipment to allow for the working space, do your collision detection and then when happy re-size back to normal (that is assuming you can resize from the centre of your pipework).
Otherwise I would say you will have to model the working space separately, check that with your collision detection and then run your pipework in that space.
And of course check for collisions again with the pipework just to be sure.
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