I faced the same issue with my DNS-343s, I use the incremental backup, but the on-board application does not support establishing rules for removing files on the backup that were subsequently deleted on the source HDD.
My solution is two-tiered. I continue to use the incremental backup and run a third party backup solution from a PC on my network once a week. I configured the software to do nothing more than delete the files on the backup HDDs that are missing on the source HDDs. The program I use is called Syncback, an exceptional application with a fully functional freeware version with an unprecedented level of rules-based configurations.