ITunes can't find some songs after update

So I've read a bit about this and it's happened to me now. I did the recent iTunes upgrade and now random song files can't be found. The " ! "shows up here and there. Now when I search for that particular song, I can find and play it. It's just that maybe it was renamed or something? I cannot manually do this since I have almost 40,000 songs on a separate HD. 99% ripped from my CD collection.
Why or how does this happen? I've been adding to my iTunes HD for 7 years or so and this was the first time this has happened.
Anyway I read a few suggestions and so I just deleted all the music from itunes BUT saved the files and now adding all of them back which will probably take 10-15 hours. It says "organizing files" wil it's a very long haul.
Will this work and will iTunes then again know where all of my songs are?

Well I researched and had to "delete" the 40,000 songs from my itunes list BUT saved the files. It took 20 hours for them to repair and then were fixed in one place with no "!" What a pain.

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