Is it possible to remove a parted out set from BrickLink inventory?
Part out the same set, but with a negative quantity.
This does indeed work, as I have solved this very problem using this solution in the past:

This is a screenshot of my Part Out Log, and you can see I've accidentally parted out 10 sets twice. Then I've reversed the second part-out.
You can see a list of every set you've parted out (after mid-2009) and the quantity in your Part Out Log.