If I'm reading you correctly, you have two copies of the your music - one on your internal storage and one on an external drive. You've tried to add the songs from the external drive but RB is suggesting you need to reanalyse.
If so - don't add from the external drive as doing this is adding a new track to the library. You would need to remove the tracks from your internal drive and then relocate them within RB.
My workflow usually is to download tracks to my local drive and transfer to my NAS before adding to RB. Then analysing/preparing cues etc.
I know you say you've backed up your library - I presume using the option within RB... which is always wise before taking any action like this.