I have many sites bookmarked and stored in the favorites bar in Safari 14.02. Some of them have subfolders or other bookmarks, and that is where the bug lies (single bookmarks in the favorites bar are not affected). When I go to a problem bookmark and select a subfolder or bookmark, the bookmark disappears from the favorites bar. When I hover the mouse over the empty space (where the bookmark had been), it reappears.
Example: There is a bookmark labelled "News" which has several bookmarked news sites. If I access one of them, "News" disappears, leaving a space but still showing the down arrow. Hovering the mouse over the space instantly restores "News".
Restarting does not resolve the issue. Other browsers (Firefox, for example) are not affected.
I have filed a bug report with Apple.