I just wanted to confirm whether or not the amount of items to win is still totaled even if I delete the line item. For example, I set my amount of items to win at 38 for a group. After a few days I deleted all of the ended auctions as I set up more bids. Do the two wins I had toward that group still get counted even after I've deleted them, or do I need to lower that threshold to 36 (if it only counts won auctions that still show on the myibidder site).

It counts the items which are active at the moment of bidding.

If your group did not meet the goal and then you deleted some items, the deleted ones will not be counted towards your goal.