Hey Jerry! 
I totally agree with you that it shouldn't broke the system, but who knows. 
What I did basically was: 
1. I quit Safari
2. Disconnect Safari on macOS and iOS devices from iCloud. (just for safari) 
3. I deleted the Bookmarks.plist on macOS. 
4. Lauch safari again and delete de bookmarks 
5. Import the old bookmarks and I keep macOS this way, so it's isolated. 
6. On iOS devices delete all the bookmarks and reading list (which are also bookmarks) 
7. Connect them again to iCloud. 
8. Add a bookmark and a reading list item on my iPhone. 
After that nothing happen at all and for awhile there was a message saying that bookmarks were syncing if I try to edit the bookmarks. 
Things were like that for a couple of days and at some point, the old bookmarks reappear on my iPad.  

I waited a day or so just to check if they will appear on my iPhone… but no. 
At some point I disconnected again my Safari on my iPhone from iCloud and connected it again… Which brought all the old bookmarks back  

A little bit after I delete some reading list items on my iPad and they started to being synced on my iPhone till I delete too much items manually and they stopped. I deleted all the reading list items on my iPad, but they didn't sync —yet— to my iPhone and I think that they are not going to sync at all and I think it's already 48h since I deleted the reading list items. 
Tell me if you have a similar behavior there or what is going on here… 
But pretty must this means that you CAN'T flush / delete your bookmarks from iCloud.