Syncing with iTunes with iPod after a massive iTunes rebuild

I have alot of music so I had to put my music on an external hard drive. When my WD external hard drive died, I had to rebuild my iTunes from my iPod Classic. I was able to copy most of my media back to iTunes by turning my iPod back into an external hard drive and then recopying the id tags back to my iTunes library. The remaining media was copied back to my iTunes library using a third party program named TouchCopy 11 from Wide Angle Software. This entire process (recopying media and relinking the media from iTunes to my iTunes library) to restore my iTunes library back to pre-crash level took two days.
So when I finished, I then synced by iTunes library with my iPod. HOLY CRAP!!!!!!!!!!!
My iPod overrode my iTunes library and totally erased all of my efforts over the past few days. Now my iTunes library has over 1000 broken links and I have to begin from scratch (recopying media and relinking).
After this process is done and my iTunes library is rebuilt, should I then restore my iPod to factory settings thereby erasing the iPod memory and then copy my "NEW" iTunes library back to my iPod.

OK, so here is my problem. I did originally download the Beta 10.10... Apparently I kept on getting betas and was running 10.10.2 (which today is still in beta).
I did downgrade to 10.10.1 (by clicking "Download" in the App Store).
Right after the downgrade everything with syncing works perfectly.
Cheers, hope this helps someone.

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Syncing with iTunes with iPod after a massive iTunes rebuild

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