Mouldings that are manually input, regardless of the vendor selected to be updated, are deleted when you select the "delete discontinued" option.
If the Moulding ID is not in the price update file, it will be marked as deleted within the database.
If a vendor updated its file and removed spaces, dashes, slashes, etc; then the Moulding ID that you are accustomed to using may have been converted to a different format and just be giving the appearance that they have been deleted.
Try running the INVENTORY: Price Update Activity report to see if the mouldings that have been discontinued are listed as NEW in the report and also New Discontinued in the report.
The good news is that you can undelete them at anytime. Tech Support should be able to walk you through the process.