This is not something you should usually have to do. However, sometimes this is just the medicine to fix media issues on a Honeycomb device. When you are seeing weird playlists issues, or new songs are missing, these steps can help you out.
The problem with clearing Android's Media Storage data is that you don't know when it is rebuilt. Luckily, iSyncr comes with the ability to let you know when Android's media scanner is running. So let's start by enabling that.