Syncing the new audio with the old is, perhaps, the key, as you suggest! I own and use Audition quite regularly but not Premiere so I have no idea whether the latter natively offers the facility you need! However, there is (non-Adobe) software specifically designed to sync two different "versions" of the same audio, Red Giant Plural Eyes It is not particularly cheap to buy, but, IMO, it does a pretty remarkable job of fully aligning two versions of the same audio! If you have Premiere, you will see from that linked page that PE and PPro apparently interface very easily You might need to first convert your flac file to wav (Audition is ideal for that) but you would then place it and the original video file into the PE workspace and press Synchronize. The software examines the files and "aligns" them (by adjusting in this case your "new" audio to exactly match the "old") and then you can have it create a new, time-aligned version of your wanted audio. You then place the original video file and the "new" (aligned) audio file in your video editor of choice, mute the original audio and export a final version with the "old" video and the "new" audio. The (manual) method you mention (time-stretching etc.) can and should achieve the same final result, but with much greater difficulty for the operator and at considerable expense of your time!
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