Okay I'm going to need to make a few assumptions :)

I will assume you are talking about thumbs in the Smart Content Pane? If this is the case what's happening is the product is gone but your database still believes it to be there just missing.

You can remove the orphan references by going to the Smart Content window and using the dropdown at the top of the tab select Content DB Maintenance Then you want to tick Remove Orphan File References then apply.

If you want to start from Scratch you can use Reset Database but this is literally a clean reset. So don't do this if there is anything you do want to retain in your CMS database.