ITunes Match has deleted my music files. How and Why?

I have used iTunes Match since January 2012 however I have noticed that fewer and fewer of my songs are available on my linked devices (iPhone, iPad). When I go to the iTunes Media Library folder to see the original files, many are missing. Typically there are only 1 or 2 song files in an album folder and the rest are just not there.
On an IOS device the songs still appear in the playlists but if selected it will just jump down the list until it finds a song that it decides it can play.
My iTunes library folder was transferred on to a 2GB network attached Lacie drive as it was too big to put on my MBP Retina in July 2012. Currently I use a 2009 iMac for the main iTunes however it is still pointing to the iTunes folder on the Lacie. MBP and iMac are authorised with iTunes store and Home Sharing is on. MBP is set to use Home Sharing, so is not syncing with Match. Apple TV 2 can also access Match and Home Sharing.
To fix this I am now working my way through a backup from June 2012 and manually checking and synching my 1200 top level iTunes folders. Honestly most album folders have only 1 or 2 tracks so I am copying back all the missing tracks one folder at a time. (iTunes has 14000 songs). I cannot merely replace the corrupt new library with the old library backup as the last 12 mths of acquisitions would disappear.
Further there are tracks that have been renamed and filed incorrectly. I have tracks labelled as Bowie or Daft Punk, in Bowie or Daft Punk playlists that are actually from an album of recordings of bird and animal sounds from sub tropical tropical rainforests. Now that kills the party when Harder, Better, Faster, Stronger crossfades into the sound of the mating call of the green tree frog let me tell you.
I have rematched my library several times over the last 12 months. When moving to the Lacie and MBP, then again when moving to the iMac for iTunes but leaving the files on the Lacie.
It's a big mess that will take me about 12-15 hours of filing to (mostly) fix. I'm up to "J".
Why and how did my original files disappear off my Lacie drive? This software/service should not have those rights.
I am a Mac fan and a college IT Teacher so run a well organised home network and am just at a loss.
Please advise.
MBP Retina 256GB 16GB 10.8.4, iMac 21" 2009 500GB 4GB 10.8.4, iPhone 4s 32GB 6.1.3, iPad2 32GB 6.1.3

iTunes Match does not have the ability to remove local files.
The service operates by comparing the selected iTunes Library with the iTunes Store content and 'matching' or 'uploading' - it is very straightforward a 'match' provides equivalent access to iTunes Store content as a recognised 'purchase'; upload simply copies a 256k AAC variant into the cloud.  There are no elements of this activity that can erase the local library content.
Would suggest you explore possible alternative causes of file loss.  Given the pattern described of selective deletion, leaving many Songs intact - would suggest making at least 2 secure offline Song file backups and starting the library again from a fresh install of iTunes once a thorough sweep of the system has been completed for virus.  It is also worth assessing the physical security of the system - who has access & with what privileges.
To access Songs from the cloud, you would have to manually delete the Song from the library or open an empty library - so even when accessing content, iTunes Match provides no local deletion capability.

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