Maybe you're seeing an MC18 bug, or maybe its something else.
Here's how I finally worked out how to best sync for my usage. I created a smartlist which includes only the files I want on my HH device (actually, it's a virtual HH, which is just a folder on a disk). In the HH options for syncing: "Check any that should be included in your sync", I've only selected my sync smartlist. All others are deselected.
Once that is done, I recheck the sync, and the list of files in the playlist are enumerated. Some will be In Queue (which means they'll be transferred), and some will be listed as On Device. Typically I have my Sync list open in one tab, and the HH open in another tab. This way, I can compare the number of files in the sync list with the number of files on the HH. Once synced, with the option to Delete on HH anything not in the sync list, both lists should have exactly the same files. An easy check is the number of files in each list.
I've worked through, and reported, several bugs, which have since been resolved in MC17. There is one remaining, but this relates to files where properties have changed, so syncing these files results in dups.
If you're seeing any issues, you may have to enable logging to track down what is going wrong.