How can I get rid of multiple versions of the iTunes Folder

Question

I am using Windows 7 and iTunes 12.1.1.4.  Multiple iTunes folders have been created on my computer (on both my C: drive and my D: drive under Users and My Documents) and they all have different content.  Some albums show up in one instance of the iTunes\iTunes media\music folder and some show up in another.  How do I get all the content synched up?  Can I simply drag and drop all these iTunes folders into D:\My Documents\My music\iTunes (the D: drive being where I store all my documents and photos) and then delete the rest of the iTunes instances?

Answer 1

Several remedies may apply:
For media files that are correctly linked from your iTunes Library, i.e., they will play without reporting something like this:
you can make sure that everything is contained within your main iTunes folders by selecting File > Library > Organize Library... and when you get this prompt:
check the Consolidate files box and, if not greyed out, the Reorganize files ... box and then click OK.  This will move any media files that are in other locations to the folders under the setting in Edit > Preferences > Advanced:
This is the location of your media folder.  By default, this will be C:\Users\username\Music\iTunes\iTunes Media, where your iTunes database (the iTunes Library.itl file) is stored in C:\Users\username\Music\iTunes.  In general that relationship between the database and the media folders should be preserved - in the example above the complete library is stored on a external drive, with the database in K:\iTunes and the media folder location being K:\iTunes\iTunes Media.  Note that this setting doesn't tell iTunes where to find media files (that info is embedded in the database); rather, this setting determines where new media is placed within the media folders.
Checking this causes iTunes to automatically place media in folders, and (re)name media files, based on the metadata associated with the files.  For music this means that everything will be in folders following the pattern iTunes Media\Music\artist_name\album_title and files to be named using the disc number (if present), track number and song name.
Checking this makes iTunes copy all new media into the media folders, independent of the method of adding it.
Second case ...
For songs that are listed in your library but you do get the "missing file" error, right-click on one of these songs - there will be a "(!)" symbol next to its name, right-click > Get Info.  When you get this prompt:
click No (there's a bug in iTunes 12 such that you actually have to click No twice).  Then go to the File tab and look for the Location information - sometimes you have to scroll down or expand the editor window to see it.  You'll see something like this:
The "file://localhost/" prefix indicates that iTunes can't locate the file.  The rest of the entry is the path to the file that iTunes holds in its database, i.e., where iTunes "thinks" the file is.  This may be enough of a clue to determine where it actually is - close the editor, right-click > Get Info again, but when you the "... cannot be located ..." prompt click Yes then navigate to and select the correct media file.  In many cases iTunes will then be able to adjust its location info for other songs.  Otherwise there are a number of techniques that you can use to track down and repair these broken links - often using scripts running against the iTunes database.
... and the third case:
If you have folders that are labeled as "iTunes" but their content doesn't appear in your library within iTunes itself, add these to the library by any of these methods:
select File > Add Folder to Library... then navigate to and select the folder(s) containing the "missing" albums/songs
drag and drop these folders from Windows Explorer into iTunes
copy these folders into iTunes' Automatically Add to iTunes folder
Once you've been through these steps its probably worth running the Consolidate Library process again to make sure everything's in the right place.  Once you've checked that to be the case, you can delete any stray "iTunes" folders that are outside the hierarchy rooted in the folder where your database and your standard iTunes Media files are located.
Two final points:
Moving files and folders around yourself never fixes anything in iTunes - in most cases it'll only make things worse by creating (more) broken links
A couple of turingtest2's valuable user tips also apply here:
Make a split library portable describes the optimal layout for an iTunes library, easing the processes of moving it between computers and maintaining a backup of it, as well as the steps needed to bring a library into that shape
Backup your iTunes for Windows library with SyncToy describes a suitable/recommended method to create and maintain a backup ... when you've gone through the effort to make your library just exactly perfect you don't want to lose it all as the result of a virus, hard disc crash, or other fatal failure!