Could you provide here or in a private message listing of files from backup index files that you mean should not be included to incremental backups? The backup index files looks like /var/lib/psa/dumps/domains/example.tld/.discovered/backup_info_2001241746/cid_user-data and can be viewed via command
zcat /var/lib/psa/dumps/domains/example.tld/.discovered/backup_info_2001241746/cid_user-data | less