Reset my iPhone just to start over fresh and see if it would fix a few very minor issues I was having and in Safari settings all of my favorites options have disappeared. Very strange. 🤔
I had some major issues with Safari bookmarks syncing when I updated this last time. They wiped and then when I tried to get them back by reloading them all on my MacBook they all appeared on my iPhone as totally blank favorites. Every time I did this they would duplicate too and none of them would delete no matter if I tried on my iPhone or Mac. Seemed like the sync state was very confused.
I fixed it after a few rounds of these steps:
1. In Safari on your Mac, export your bookmarks to an HTML file (File > Export is the path I believe)
2. In iCloud settings on your iPhone, turn off the Safari option for "Apps using iCloud" and choose to delete data
3. In Safari on your Mac, edit your bookmarks and delete them all
4. Wait a few minutes to see if they come back; you may need to delete them a few times
5. In iCloud settings on your Mac, turn off the Safari option in a similar manner you did for your iPhone
6. I completely closed Safari on my Mac and iPhone at this point, waited a few minutes, and then opened them again
7. Make sure both devices still have no bookmarks in Safari
8. In Safari on your Mac, import your bookmarks from the HTML file and then move them into your desired location
9. In iCloud settings on your Mac, turn back on the Safari option and wait a few minutes to see if they stay correct
10. In iCloud settings on your iPhone, turn back on the Safari option for "Apps using iCloud" and choose to merge
11. Hopefully your bookmarks reappear on your iPhone and now sync properly again
I had to do the "turn off, delete, import, turn on" cycle twice before everything worked. I see you have an iPad also so you may need to include that device in the steps when turning the option off and on for Safari in iCloud; I'd just turn the option off on the iPad at the same time as the iPhone, but wait to turn it back on until your Mac and iPhone are syncing.