Do I need to wipe my iTunes library?

I had installed OS 10.9.2 on a blank new hard drive, and laboriously pulled over parts of my iTunes library from my old drive into iTunes 11.2. Then something came up that I had to wipe the new hard drive and reinstall the OS. Wanting to hang on to all the iTunes work I'd done, I copied the new drive's Books and Music folders from iTunes 11.2 to my old drive for safekeeping until the reinstall on the new drive. By the time I got around to reinstalling the OS on the new drive, it was OS 10.9.4 and iTunes 11.3. So those got installed.
When I copied the saved Books and Music folders to the iTunes 11.3 folder, my playlists didn't show up. (As I now know, I should have copied yet another file to save the playlists, but it's no biggie to re-create the playlists.) The odd thing is that some of the albums I'd had before didn't show up either. For example, in one  artist's folder within the iTunes folder structure, there were (and still are) 5 albums, yet only 4 of them show up in iTunes 11.3.
So I added a fresh copy of that album to my library. All of a sudden iTunes saw that album and showed 2 complete sets of that album's tracks, iTunes having appended " 1" to the names of one set and dumping both sets into the 5th album's folder. Um … not what I hoped would happen.
The same thing happened in the case of another missing album, and I imagine there are more such cases in store for me if I don't stop that approach.
What should I do? Wipe the entire iTunes 11.3 library and do the laborious pull-over again? I'm willing, but please tell me how to wipe it.
Alternatively, can I dive into the iTunes folder structure and remove the troublesome albums, then add them again via iTunes Add to Library? I'd prefer this approach, but I don't know if such manual intervention in the iTunes folder structure is going to mess up everything.
Please advise. Thank you.

gyandev wrote:
Got the answer from another forum. It's ok to use the back door: dive into the iTunes folder structure and remove albums that are there but iTunes isn't seeing, then add them again via Add to Library. iTunes didn't miss a beat when I did that. Whew!
Better yet, leave them where they are in the iTunes media folder and simply add them to iTunes.
File > Add to library and select /Music/iTunes/iTunes media/ folder.

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