How timely. I was running into the same issue. I tested a few things to confirm what you wrote and exactly how it was corrected. This is what I am doing, step-by-step.
1. All my products (I have thousands) have been imported, not manually created one-by-one. First the product variation import, followed by the product node import.
2. I delete the imported product nodes. This appears to also delete the product variations, because if I go to my product variation import after running the delete for my product nodes, a message displays "There are no Commerce Products to be deleted."
3. After making the fixes to my csv file, I then run my product variation import. A message displays, "Created 1000 commerce products.'
4. I run my product node import. A message displays, "Created 1000 nodes."
5. I checked my items and the last integer in the product URL has increased by "1".
6. Then I tried it in reverse. I deleted the product variations. When done, I deleted the product nodes (using the delete feature of the import user interface).
7. I re-ran my product variation import, followed by my product node import.
8. I checked my items and the last integer in the product URL did not change this time.
My issue now is that I've run this so many times, that the integer "3" is appearing after the dash. I can't seem to get back to "-0". Basically, I need to be able to delete ALL product variations and ALL product nodes for the category I am working with.
Thank you for your help on this!