If it's showing as overdue that usually always means that the order was never marked as shipped and tracking was never added. I'm assuming you are using POD Production Partners. If so then it's always a good idea to check orders every day to make sure everything is syncing properly between your etsy shop and your POD partner. The issue you are dealing with is a perfect example as to why it's important to keep tabs on things every day. The integrations between the 2 aren't 100% reliable and bugs can and will happen from time to time.
As far as how to deal with it...you have a couple of options.
1- you can get the tracking number from your printer and mark the order complete and manually add the tracking info. Note that if you go this route the system will automatically send your buyer a "your order shipped" email so I would be sure to add a note to your buyer about it.
2- since star seller bits are only a 3 month period of time the order won't count against you forever. You could just move it to a custom progress step on your orders manager page to get it off of your open orders page.
Oh and if you are using a POD production partner be sure that you have declared that properly as required.
