Hello everyone,

I'm recording a song where I do a guitar harmony and have two different recorded guitars playing different notes. However, as you would expect, it sounds very different than the parts that just have one guitar playing. Is there a way to get rid of the doubletracked sound in my recording?

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Phase-align the two tracks, time-align them if necessary.
If that + a bit of mixing doesn't work then you have to re-record something 'cause the tracks you have now are not good enough.
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Sounds like an arrangement issue, not mixing. When you add in and take away a whole melody instrument, it's gonna be noticeable. You can make this less jarring by mixing it down low, but you'll lose some strength when it's in there.

Your best bet is honestly to write another part for that guitar to play in other sections - not necessarily a harmonized lead, but maybe something that can sit in the background and contribute to the rhythm, but not necessarily another rhythm guitar track, if that makes sense (not chords, a rhythmic lead).
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automate the levels so that the volume stays consistent between parts. You're probably just dealing with your doubled guitar part being louder than the single guitar part. Proper levels is very important when stacking guitar parts - you may also have to eq the second guitar to cut some frequencies.