Files copied (backed up) on an external hard drive can NOT be opened

MacBook Pro (2.5GHz, intel Core i5)
OS X Yosemite, 10.10.2
I was running low on storage space on my Mac Pro. I copied all items on Desktop to my external hard drive. After all files were copied from MacBook Pro to the external hard drive, "get info" suggested that the amount of space taken entirely was the same between when all items were on the Desktop and when they were on the external hard drive. The number of items copied over were also identical. I should have been more careful, but I then deleted all items from the Desktop. It was until a few days later (today) that I noticed majority of the files copied over onto the external disk can NOT be opened now. The error message was "The alias “<filename>” can’t be opened because the original item can’t be found.".
I really don't want to lose these files, but where are they? They got their file sizes correct but just can not be opened. I tried copying these files back to Desktop on my MacBook Pro, that's not helpful. I tried accessing the files on a PC, still can't open the files. I tried repairing disk of the external hard drive (under Disk Utility), still can't open the files. I tried repairing disk permissions of my MacBook Pro hard drive, still can't open the files.
One last thing I tried in terminal (I am not terminal savvy at all, just googled the "The alias..." error message and copied the instruction):  /usr/bin/SetFile -a a /Volumes/MAC This did not solve the problem, either.
Thank you for your help in advance!

Hi, eddie from pataskala ohio.
We love pro-active thinking here at the Apple Discussions and you're off to a great start.
Even though upgrading iTunes shouldn't affect your Library, one of the funny things about computers is that sometime, somehow, somewhere when you least expect it , they can do some not so funny things, like losing data that they're not supposed to. Which is why it's a good idea to have a back up copy of any data (such as your music) that you value in reserve ... just in case.
The most straightforward way, is to go to the iTunes Edit menu > Preferences > Advanced tab > General sub-tab and make sure your iTunes Music folder is assigned to its default location: C:\Documents and Settings\User Name\My Documents\My Music\iTunes .
Next make sure all your music is stored in that folder by using the iTunes Advanced menu > Consolidate Library option.
Now you can copy the entire iTunes folder - the iTunes Music folder and the iTunes library files in particular - to your external drive.
If anything does go wrong with the upgrade, you'll be all set to recreate your Library.

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