I'm sure someone who is better versed than myself will come along, but there was a thread a little while ago along these same lines.  When I read it, I immediately went into damage control, (fearing the worst) and basically checked all my stock for Variation listings.  In a nutshell, it seems that even when a Variation listing runs it's full course - in my case 30 days - regardless of what has been sold during the 30 days, if you Re-List it will do so using the original quantities - a right pain in behind !

I now re-list Variation listings individually so I take note of remaining stock when listing ended and then ensure (hopefully) I re-list the remaining quantities only.  I had always assumed (oops, should know better than to assume !) when re-listing an ended listing it would relist remaining stock only - often wondered how/why I could not find items I had listed, but I do always try to keep back up stock to cover any lost in transits etc so have never actually been caught out thank goodness.

As I said, I'm sure someone will come along with a better explanation, particularly in regards the stock control side  . . . . . . . . . .

Meanwhile, as they say, you learn something new everyday