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The way to help with (3) would be to make sure that the file you upload starts at exactly the same spot as the file TNG uploaded. Like, exactly. Last time, your two files didn't even start in the same place. You should be able to import what you upload into a new project right next to the old project and hear no flanging, no phasing, no delay, nothing. Theoretically you should be able to invert phase on one track and have it cancel out the other. ptf is a pro tools project format. It's old. It's what TNG uses. The rest of us moved on to .ptx like 4 years ago.