I'm sure someone with way more expertise than me will come along, but from my experience with Variation listings, I'm pretty sure you could, but it will basically mean revising and re-doing almost the entire listing.  In other words, you will need to delete that item as one of the variations, but then you will need to re-enter prices, quantities and all photos for the remaining items.  A pain in the proverbial in other words   But pretty sure it can be done - good luck ! 

 

I guess it depends how many items are involved & how long the listing has to run if it's worth the hassle . . . . . .

In my experience, setting a variation to 0 quantity will have it removed. However, if you have sold any of that variation, it can never be removed.

I have the same problem, I just have to live with the [out of stock].