Are these photos taken on the iPhone, then imported to the Mac? If so, that's where it's going to hang up.
Photos "Sync" is a one-way street Mac to Phone. When you move photos from iPhone to Mac they're not synced but rather "Imported." There's an option to "Delete from phone after import" so if you want the Mac to control what's on the phone, you should use that to completely wipe the photos off the phone. Then you can "Sync" photos back from the Mac to the iPhone (using albums or whatever filtering method you want). If you then later delete a photo from the Mac, that WOULD delete it from the phone since the only version of the photo on the phone was synced from the Mac.
The other option, of course, is iCloud Photos. That's how I've chosen to set mine up and it "just works"; I can make any changes (edit a photo, add/remove from album, add a photo, delete a photo, etc) on any of my devices and it syncs automatically to all of them (3 Macs, an iPad, and an iPhone). There is no equivalent to that feature using USB sync.