dual boot problem in win 98/2000

Do you have a software that can correct the following problem?? where can I buy it? How much?

I have a Dell L733r tower with dual boot in win 98 and win2000.

By mistake I did scan disk in win 98 with auto repair. This terminated all long folders in win
2000 making them *.chk extn. and no more possible to access them. [about 20 GIG] . I can not open
the .chk files as word will open it but in machine type language.

Is it possible to undo the scan disk ? convert the .chk files back to the folders and reaccsess
the win 2000? If not how to read .chk extn. files and save the data before I clean out the Hard
drive with a fresh installation?

At present I can access some data by installing win 98 on the same HD but in a different folders.
[I have now 2 versions of win 98]

Thanks for your help