OE can be such a pain in the a** sometimes. Assuming we can find them, we should be able to get them back. First of all, log in to OE and go to Tools>Options, Maintenance tab, click Store Folder and either copy or write down the exact path. Now, browse to that path in My Computer. Do you see the missing folders there? If they were deleted by someone or something, ended up in your Recycle Bin and then Restored from the Recycle Bin, they should be there.
Do you see them? If not, the instructions below do not apply.
If so, here's the easiest way I can think of...
The problem is that OE has lost the link to that file even though it exists in the folder. So...
Open OE, create a new folder named Test. If you need to get 3 folders back, then create 3 folder naming them Test1, Test2, etc - however many you need. Now, close OE, browse to that folder again and delete the Test folders (remembering the exact name) and rename the *missing* folders files to those Test names.
For example, if one of the missing folders was named MyStuff, you should see a file named MyStuff.dbx in the path you browsed to. Open OE, create a folder named Test1. Close OE, delete the Test1.dbx file in My Computer, rename MyStuff.dbx to Test1.dbx and open OE again. You should now see all emails that were in MyStuff.dbx in Test1.dbx. You can rename the folder back from within OE.