You should not need to repartition just yet - check the file system. There are quite a few threads on TMO and possibly some mention in the Wiki. Essentially, you first "unmount" mmcblk0p2 (i.e. the MyDocs partition), then you perform the check and lastly turn the phone off. When you turn it back on, it will all be OK.

Look it up because it's worth remembering the command terms - there are only two or three and they're quite short.