I see what you mean. The Default setting is set to: Do Not Remove instead of Remove. This will be corrected in the next BPS Pro version release.
Ok since you have a lot of files then just delete the entire ARQ Add Database Table and then manually delete the files via FTP.
Go to BPS Pro Pro-Tools and click on the DB Table Cleaner/Remover tab. Select the wp_bpspro_arq_add Database Table and delete it by choosing Drop or choose Empty to delete all Database Rows, but leave the DB Table.
The bps backup added files folder is located here: /wp-content/bps-backup/autorestore/added-files/