Yep, here's how it works. If you own at least one paid plugin for a certain bundle, you will be able to complete that bundle. Whenever you complete a bundle you pay only for any plugins you do not already own. The price for each of these plugins is calculated using the same bundle discount as the whole bundle had initially, as a percentage. So if you were looking at a bundle that had a 40% bundle discount, each product you miss will have that same 40% discount applied.
So make sure to always log in to see your available completion prices.