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I am doing swapping out a tired B6 enigne with a low km import.
Is there anyway of removing the engine just by unbolting the compressor and leaving it in the engine? Has anyone done this before and not bent the aluminium pipes? Or am i better to drain the air con system and take out all the piping?

I think you want to know if you can just leave the air compressor in the engine bay??
YES you can.

When we just did our engine swap, we just tied it to the side so it would not get in the way when we put then engine back in.

As Dweezle said, you definitely can. I undid the power steering reservoir as well and cable tied it all out of the way.
Then you dont have to ungas and regas the system..

Certainly helps to have another set of hands to hold it in ther right spot when re-installing the engine though.
I put the engine in by myself and it was a pain trying to hold everything at once so it all aligned properly.