Changing the media folder path tells iTunes where to put new media that is ripper or purchased. It may offer to consolidate to the new location when you make the edit, if not iTunes will expect existing content to remain on the original path.
The "missing file" error happens if the file is no longer where iTunes expects to find it. Possible causes are that you or some third party tool has moved, renamed or deleted the file, one of its parent folders, or the drive it lives on has had a change of drive letter. It is also possible that iTunes has changed from expecting the files to be in the pre-iTunes 9 layout to post-iTunes 9 layout, or vice-versa, and so is looking in slightly the wrong place.
Select a track with an exclamation mark, use Ctrl-I to Get Info, then click No when asked to try to locate the track. (Due to a bug in iTunes 12 you currently have to say No twice!) Look on the summary tab for the location that iTunes thinks the file should be. Now take a look around your hard drive(s). Hopefully you can locate the track in question. If a section of your library has simply been moved, a folder renamed, or a drive letter has changed, it should be possible to reverse the actions. If the difference between the two paths is an additional Music folder in one path then this is a layout issue. I can explain further if that is the case.
In some cases iTunes may be able to repair itself if you go through the same steps with Get Info but this time click Locate and browse to the lost track. It may then offer to attempt to automatically fix other broken links.
If another application like Windows Media Player has moved/renamed the files then the chances are that subtle differences in naming strategies will make it hard to restore the media to the precise path that iTunes is expecting. In such cases, as long as the missing files can be found somewhere, you should be able to use my FindTracks script to reconnect them to iTunes. See this post for an explanation of how it works.
For more background on the typical layout of the iTunes library see Make a split library portable.
1) It depends on exactly what you have done to break things.
2) Your media files are where you put them, or where iTunes copies them to when they are added to the library. If multiple libraries use the same set of media folders there can be problems if edits in one library cause content to be moved as the other libraries will no longer see those tracks on the original path, and won't know to look in a new one.
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