So long as the system drive is separate, you can reinstall the software, and the media will be kept intact, and will be re-detected upon bootup again.
There is one little fix, that you must do. I am assuming you set up your RAID to use LinuxMCE's file structure?
After installing, go into the web admin > Advanced > Devices .. you will find your Software Raid device detected. Select it, and scroll down to the bottom.
Change the PK_Users setting to Use LinuxMCE File Structure. Save, and then reload router. Your media will be crawled again.