It depends on where you are seeing the folders missing in File Explorer. is it in the left Navigation pane, or are the folders missing in Quick Access if you click Home in the left pane?
1
If the problem is in the left navigation pane, right click an empty spot in the left pane and toggle on/off some of the available options to test if that brings back your preferred view in the left pane.
2
If the problem is in the Quick Access section when you click Home in the left pane, you may need to re-pin folders to Quick Access.
Find one of the missing folders, then right click it and select 'Pin to Quick Access', does that folder then re-appear in Quick Access.
3
If that does not resolve the problem, please provide a screenshot of your File Explorer window indicating where the folders are missing from.