Having painstakingly deleted hundreds of unwanted photos, dare I re-sync another Mac to iCloud that still has many of the deleted ones?
There’s no risk if you have a backup. Cloud syncs, just like RAID are not backups.
I’ve had very good experience with Apple tracking when I delete files from a fully health sync setup. Adding a new device to sync generally wants to combine all.
Also - look at a tool that can easily clean duplicates if you run into this situation often.

https://fatcatsoftware.com/powerphotos/

If you want to be safe, set up a new photo library or export all the photos before you start. Designate the empty library as the system one and then go slowly once you’re sure the sync is solid.

https://support.apple.com/en-us/HT204414