ITunes upgrade then cannot locate source file

It seems everytime I update my iTunes it loses the source location of my music. 
I have an external drive that has over 16k music files.  I don't understand why.  At least I checked after the update before I started adding more tunes.
I recall this happening once before and when i clicked through to locate the source, I ended up with duplicates and a very full local HD.
I've treid searching countless threads for a solution, but it seems most issues are related to erroneous moving of files, or some other issue.
What should I be doing?  Why does it always change my media file settings and advanced settings?  What is the best way to correct this during upgrades.   I'm so frustrated with music suddenly starting to be imported to my local HD and not my external drive.  
Things I make sure of:
External drive is always connected and recognized before starting iTunes.
All music is in one location, Music Master folder on external Drive.
What is best practice/process to deal with continual issue?

The "missing file" thing 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, or that 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 cancel when asked to try to locate the track. 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, or a drive letter has changed, it should be possible to reverse the actions. I can provide a step by step guide if you give me the two paths.
Alternatively, as long as you can find a location holding the missing files, then you should be able to use my FindTracks script to reconnect them to iTunes.
tt2

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