I found the solution!
Go onto your Facebook - Shopify commerce account (the commerce manager), click catalog, then items. From there, click on whatever product you want to delete.
There'll be a pop-up for the item and in the top right, click delete.
I was having these same issues myself, but with some digging around, I was able to remedy the isuue.
Best of luck, and I hope this worked for everyone!
Same problem, doesn't sync deleted items, the worse thing is, that facebook shop say that they are in stock... But they never were in stock. I thought that the products should by synced by shopify app, so if I need to delete every product myself manually (more then a hundred...) I will be very disappointed. IS THERE A WAY, or an app that works and completely syncing my shopify store product catalogue with facebook shop??