Hi Resist,
It sounds like you've done well with isolating the issue. When adding the favorites back were the steps below found in the article here used? Add websites to your Favorites in Safari on Mac - Apple Support
"You can quickly see websites you access frequently by adding them to your Favorites, so you can get to them with just a click.
- In the Safari app
on your Mac, move the pointer over the Smart Search field. - Click and hold the One-Step Add button
that appears at the left end of the field, then choose Favorites.
You can also click in the Smart Search field, then drag the URL of the website you’re viewing to the Favorites bar near the top of the window, the Favorites folder in the sidebar, or the Favorites area on the start page."
If so, and the issue continues reach out to Apple Support directly to further assist.
Contact - Official Apple Support
Contact Apple for support and service - Apple Support
Best.