In the past there have been SKU prefix changes at Turn 14. They sent out an announcement about the changes prior to the update. They were retiring some old SKUs and replacing them with new ones. The affected brands were deleted because the SKUs look "abandoned"; but then those brands were reloaded with the new SKUs - so you don't need to do anything.
The app automatically updates your store to keep it accurate; however you may feel concerned if you notice the app deleting products, and/or if you have updated or customized some products manually and these are getting deleted or overwritten with the new SKUs.
To avoid losing customized products you can chose an option in the filters tab "Disable the removal of filtered products".