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One of the key features of iHomeServer is that it performs media cleanup in the background.
This was designed because one of the key aims of iHomeServer is to allow you to add, change and delete media on your media server remotely without having to manually tell iTunes about the changes. If you rename a folder in your media collection, iTunes doesn't know about it. iHomeServer doesn't know that you have done a rename either - however, it does spot new media that it doesn't know about. Therefore, it will add the new folder name to iTunes.
However, as iTunes doesn't know this was a rename, it will have a duplicate (old) reference to the media in its library, pointing at the original folder. iTunes is smart enough to know that this folder no longer exists, but doesn't know whether this is temporary or permanent - therefore it leaves it in the library but removes the reference to the file.
iHomeServer scans through the iTunes library looking for files with no references (i.e. where iTunes cannot find the source media file), and automatically removes the stubs from your iTunes library. This allows you to move content around within your Watched Folders and iTunes will keep in sync automatically.
The one disadvantage of this cleanup is that if you store your media on removable storage (or storage that is not guaranteed to be there, like a NAS), if the clean-up occurs whilst that media is unavailable, it may be inadvertedly removed from your iTunes library. When the media comes back on-line, iHomeServer should spot the media and re-add it back to iTunes. However, if you want to avoid this behaviour, you can disable the cleanup by unticking the checkbox "Delete orphaned tracks automatically" in the iHomeServer Configuration tool.
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