Restore not replacing music.

Nearly two years ago I upgraded my handset from the iPhone 4 to iPhone 5. I backed up the 4, got the 5, and did a restore. When I did the restore it added all my music. But when I went to iTunes on my laptop all the music I had imported from my CDs had disappeared And all that was there were my iTunes Store purchases. My phone still had the imported music though. Zoom forward to now, I had my iPhone 5 replaced due to faulty battery and diligently did my back up and restore as instructed by Apple. This time no music restored at all so I have lost ALL my imported music and don't know how(if) I can retrieve it (my iTunes purchased music was easy to restore). Can anyone shed some insight on why/how this happened, how I can prevent it in the future and if I can retrieve my beloved music that I cannot replace?

There is nothing that you can do with an iPhone that will remove imported or ripped music from your computer. If your music is gone then you have computer problems, not iTunes problems. I've been ripping music for over 10 years, and all of it is still in my iTunes library, even though it has been moved 4 times to newer computers.
However, music is NOT part of your backup. To restore music to a new phone you first restore from backup, then sync the phone. The sync will restore your music unless you have Manually Manage... enabled, in which case you will have to manually manage it again. Which is why Manually Manage is an abomination. The better way is to create an iPhone playlist, drag the music you want to the playlist, then sync the playlist with Manually Manage turned off.
In general for moving the data on one phone to a new phone see: Transfer content from an iPhone, iPad, or iPod touch to a new device

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