Why would ProductCatalog sync with Force Update selected completely remove all instances of a custom item type from the DB?

I am using BundleTemplates and have created a custom item type and a relation between BundleTemplates and my item type. When I do a product catalog sync without Force Update selected, these custom items are not removed. When I run the sync with Force Update selected, the items get completely removed from the system. Does anyone know what would cause this?