I believe I found a more efficient solution than the last one mentinoned (provided that you have a vaild backup of the .eml files in another folder. If you don't and you are sure that the mails themselves in the bad indexed folder are not corrupted -meaning that when you double click on them they open and they are correct- make a copy of the .eml files to another folder):
in WLM create a new folder, with no messages. Leave the WLM open showing that new empty folder. Then, in Windows Explorer, locate the backup folder with the .eml files and drug'n'drop them into the newly created folder in WLM. After you have double checked that you have transferred all your corrupted emails to the new folder you may safely delete your bad indexed folder. Repeat the process for every problematic folder.
The above was tested in WLM 2012 but I strongly believe it will work on WLM 2011 also (maybe on older versions too).