If you want to delete a product that has several variations on eBay, here are some options.
Make sure you only delete them using the red wheel icon on the right side of it's line in the monitor and NOT with BULK OPERATIONS button:
After clicking the Delete button in the product line on the monitor, a window will open where you can select the following options:
If you want to delete the whole listing with all its variations from eBay and the monitor, you must check the two "V" in the delete options panel:
2. If you'd like to delete just a particular variation from the listing - you nee to check "V" only on the left box:
3. If you'd like to delete all the variations of your listing only form the monitor - check the right "V"only: