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 in Settings > Media Scanner > Notification.
With the notification enabled, we will now clear the data for the Media Storage database. Let's start by opening the settings.
Once in the list of all applications, just scroll down to select "Media Storage"
Finally, we get to the Media Storage and can press "Clear data". This does not remove any media from your device, but does clear the database that most applications use to look for new songs, playlists, photos, etc.
Now that we've cleared the cache, we will rebuild it. For this step, you will need to reboot your Honeycomb device. Just hold down the power button and choose to power it down. Then turn it back on. Once it reboots, you should see the notification in the following picture. Once that notification goes away, the cache is rebuilt and you can continue using your device like normal.
That's all! Just let us know if you any further questions.