This worked for me
My situation was similar to some. I had two devices listed in my iTunes wifi sync area on my iPhone 5S. Both were my Mac Mini. One had all the items I chose to sync (Apps, Books, Movies, Photos, and Tones). The other had no items listed. It's "sync now" icon was also greyed out. But, it was annoyingly there. The only thing I could hypothesize that created this rogue 2nd sync device was when I chose to uncheck the option in iTunes..."Automatically Sync when this iPhone is connected." I did that because I was using a piece of software (PhoneClean Pro) that had its functionality compromised when my iPhone started to auto sync at the end of its data cleaning procedure. I am guessing that iTunes recognized this new setting for syncing as a "new computer." So it created this new syncing device in iTunes Wi-Fi Sync...even though this "new" device was still my one, and only one, computer...my Mac Mini. OK, that is the background. Here is what I did to remove that second device...leaving just that one Mac Mini in the iTunes Wi-Fi Sync area that had all my syncing items listed.
1. I made a "backup to computer" of my iPhone. Not a iCloud backup...although I did backup to iCloud for good measure
. I wanted a complete backup as I was going to do a "Restore FROM BACKUP." iCloud backs up only the most important items on your iPhone. I wanted everything...including my app folder organization scheme so it could easily be recreated in the restoring process.
2. I clicked on "Restore" in the top right corner of the iTunes screen. You have to turn off "Find my iPhone" before doing this. If you don't...not to worry. iTunes will prompt you to turn off "Find my iPhone" if you forget.
3. The restore process began. This is not a 2 minute deal so be patient. When the first part of the restoring is finished you will get a prompt as to what backup you want to restore from...choose that last Backup to Computer you did in #1.
4. At this point all your data will be transferred back to your iPhone...apps, music, app folder structure, etc. This is going to take a while...especially if you have a lot of apps, music, etc. I'm talking a couple hours.
5. Once this process is complete you will have most of your iPhone back just as it was. You will have to sign back in to some things. But, in general, because you restored from backup you will not have nearly as much to do compared to if you Restored your iPhone as NEW.
6. You will also notice that if you go to General-->iTunes Wi-Fi Sync you will only see ONE device. The device on which you did the restore...in my case, my Mac Mini. Those extra devices will be gone.
7. Not only did I have "Automatically Sync when this iPhone is connected" unchecked. I also had "Sync with this iPhone over Wi-Fi" unchecked before starting this process.
8. My last step was to turn back on "Sync with this iPhone over Wi-Fi." BTW...all this is being doing with the iPhone connected to my computer via USB. I then clicked on "Sync Now" on my iPhone in "iTunes Wi-Fi Sync" with the USB cable still connected. Then I disconnected the USB cable and redid the procedure in the previous line.
9. All is now good. My iPhone syncs over wifi and I have only one device listed in the "iTunes Wi-Fi Sync" page.
There is more waiting than hard work involved with this procedure. So, don't make a go of it until you have some time on your hands to keep an occasional eye on your computer while the process moves along. Certainly, if you want to clean some toilettes and a couple loads of wash as the same time you are good to go for than kind of multitasking.
Hope this is some help to others.
Cheers, Mr. Luigi