Songs on iPod are grayed out and purchases in iTunes are missing

So my mom's having some trouble with iTunes-
When her 7th gen Nano is plugged into iTunes all of the songs on it are grayed out and unplayable. There are no icons or such that suggest that there is a problem.
She has 559 songs on her iPod that she purchased and downloaded with the same Apple ID that she still uses today, however iTunes says that she only purchased 179.
This problem must have started when the computer she uses was wiped and had Windows 7 re-installed, but this shouldn't affect the data associated with her Apple ID?
Is there anyway that the songs on her iPod can be transferred to her library? (after they're somehow ungrayed)
Any little bit of help is appreciated

With manual transfer you drag the songs from your iTunes to the iPod. That's how manual works and has nothing to do with songs being "check marked".
However, this is an extremely risky option because when (and not if) there comes a time to restore your iPod, which is a very common fix for iPod problems, then all the music would be erased. If you no longer have the music in iTunes (or any other back up), then all that music would be lost.
What if the iPod were lost/stolen/needed repair? Again, the music would lost. I strongly recommend a back up, and if computer hard drive space is in short supply, you should seriously consider an external hard drive. They are not expensive, and the cost is well worth it when compared to the loss of all your precious music.
At the very least back up your music to either cd or dvd before deleting it, particularly any purchased music/videos, as this would have to be bought again if it were lost. See this.
Backing up your media in iTunes.

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I recently transferred itunes library from windows XP PC to new Windows 7 PC. The transfer was successful, however when I plug my 3rd gen Ipod Nano into the new PC, the Ipod icon appears along with the music, playlists, etc. The songs are shown but are 'grayed out' and wont play or sync.The 'Devices & Printers' window in new PC shows icon for Ipod driver & is OK. The icon for the Ipod appears but depicts a delta shaped warning icon that states that the Ipod is'not operating properly'. Tried troubleshooting. The troubleshooting message states the the Ipod is 'disconnecting'. Can you help me with this problem?

Then, I dropped the entire itunes file from the old PC (XP) into an empty external drive.
That "itunes file from the old PC"? Is that the iTunes folder, from the old PC, that was in the user home folder's Music folder?
All of the library, playlists, etc. from the ipod as they always have been are shown, by they are 'grayed out' and will not open or play.
That's on the iPod, correct? Are all of your old playlists in iTunes, from the old PC, still there in iTunes on the new PC? Are the songs in iTunes still playable?
This document provides the steps to transfer a complete iTunes library between two computers. See the section called External drive.
iTunes: How to move your music to a new computer - Apple Support
There are many steps, but this is a summary. (1) On the old PC, consolidate all of your iTunes data into the iTunes folder. (2) Copy this iTunes folder to the external drive. (3) On the new PC (that has iTunes installed but NOT running), replace its existing iTunes folder with the one from the old PC (on the external drive). When you run iTunes, it uses the iTunes folder from the old PC, and it should look like iTunes on the old PC (with all the playlists, ratings, play count, etc.), and your iPod will see the iTunes library as the same iTunes library (because it is the same library).
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I had this problem too and my roommate solved it!
Go to 'Settings'
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Lack of support from that company seems to be a non-uncommon problem. But it's not a problem you will be likely to get help with in the Communities, and definitely not here in the "Using Apple Support Communities" forum which is for questions about the Communities themselves. If MacWare can't or won't help you, you may be stuck, though there was an email address posted in this thread:
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So itunes is giving me problems. Since around Christmas time, itunes decided to stop reading my ipod. I connect it to my computer with the usb cable and my computer will recognize that a device is connected but itunes will not. If I go to file->devices and try to sync, all of my sync options are grayed out, while before it would just automatically sync.
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Do the USB ports work for other devices?
Does the iPod charge?
See
iOS: Device not recognized in iTunes for Windows
- I would start with
Removing and reinstalling iTunes and other software components for Windows Vista, Windows 7, or Windows 8
However, after your remove the Apple software components also remove the iCloud Control Panel via Windows Programs and Features app in the Window Control Panel. Then reinstall all the Apple software components
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iOS: Device not recognized in iTunes for Windows
paying special attention to item #5
- New cable and different USB port
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iTunes for Windows: Device Sync Tests
Also see:
iPod not recognised by windows iTunes
Troubleshooting issues with iTunes for Windows updates
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I am having the same problem. I have many dark icons that say waiting. I can't do anything with them. I can't even delete them because they do not get the little x on the upper right corner like the light apps get. I do not know what to do. If I call Apple they will charge me for support as my phone is over a year old.

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How much space is used by your Other? You may be able to reduce.
How Do I Get Rid Of The “Other” Data Stored On My iPad Or iPhone?
http://tinyurl.com/85w6xwn
How to Remove “Other” Data from iPhone, iPad and iPod Touch
http://www.igeeksblog.com/how-to-remove-other-data-from-iphone/
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https://discussions.apple.com/docs/DOC-5142
iPhone or iPad Ran Out of Storage Space? Here’s How to Make Space Available Quickly
http://osxdaily.com/2012/06/02/iphone-ipad-ran-out-of-available-storage-space-ho w-to-fix-quick/
6 Tips to Free Up Tons of Storage Space on iPad, iPhone, and iPod Touch
http://osxdaily.com/2012/04/24/6-tips-free-up-storage-space-ipad-iphone-ipod-tou ch/
Also,
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http://www.igeeksblog.com/how-to-clear-message-imessage-cache-on-iphone-ipad/
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http://support.apple.com/kb/ts4054
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http://support.apple.com/kb/PH12113
iTunes 11 for Windows: Set up syncing for iPod, iPhone, or iPad
http://support.apple.com/kb/PH12313
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http://support.apple.com/kb/HT1351
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Songs on iPod are grayed out and purchases in iTunes are missing

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