I doubt that they are "lost", just not connected with your current
Favorites location.
Here's what I would try:
1. Open an Explorer window at your current Links location.
Alt-a,L,CursorLeft,Menu-O,Enter (If you prefer to use the mouse
click on the Favorites menu label, right-click on Links,and select Open.)
This will be your copy target.
2. Find the old Links folder. Was it on another partition?
Press F3 to open a find window and find that other Links folder.
If you're not sure where it was start the search over all Local drives.
Customize the search so you are looking only for files of type Folder
and make sure that you can see all files and folders.
3. You can open what you think are likely source candidates in their own
Explorer windows by pressing Shift-Enter.
4. Select the items you want to copy or press Ctrl-a to select them all.
Prepare them for copy with Ctrl-c.
5. Either open the Links folder of your target separately too or click Back
on the search window.
6. Press Ctrl-v to paste the selected items into the target folder.
Note these instructions were prepared while looking at XP.
You haven't disclosed your OS so if it is not XP don't be surprised
if you have to find some adaptations to them.
I'm not sure how quickly IE would become aware of these changes.
You might have to close it and reopen it again.
Good luck
Robert Aldwinckle