When you speed up a track, it's going to get shorter. If it matched another track before being sped up, then the other track will be longer than the one that got altered.
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When you have two tracks that start at different times, you need to find TWO sync points common to BOTH tracks. The further apart the better. Consider one of the sync points your new 0 (ZERO). Basically a two step process, make them run at the same speed (no drift), then trim each to same sync point / point in time. Bear in mind that you'll likely need to re-find the sync point (zero) after resampling. Could be simple math and automated. Could be going through the ID stage a second time. Which you should probably do to verify results anyway.
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I agree it's not something that I should have to do. But in my case the drift is so small, and the tracks / hardware so closely related, that any variance in temperature will likely not produce a variance in clocks and drift large enough to be of concern. And probably not that adjustable anyway depending on the decimal point accuracy of the CPU/FPU (and software) performing the conversion.
I've got a process now and it seems to work. sndfile-resample is my friend. And audacity his good buddy. I still need to find an equivalent to sox's trim function, manually punching in the timestamps is a bit tedious IMO. Resampling happens first and relatively blindly / on faith. That way the gui only loads small and manageable files. I'm loving the results so far. Finally something put the Tuba player back into the brass quintet. I've tried all scores of EQ and other tricks to limited success until I figured this one. I even tried a few different mics which generally proved more problematic. I've listened to these things many hundreds of times and it's bugged me every time, until now. It's like I got a $500 or would it be $5,000 upgrade. Since it looks like I wont need to try those $3K+ mics in an effort to keep my sanity. At least not anytime soon.
I've still got to track down what's the root cause. It shouldn't be the hardware as that would be problematic when it creates new files after every 12:41.2??. Lot's of A/B-ing in my near future I guess, to see if audiogate and only audiogate satisfies. I've generally left it to audiogate to convert from DSD to an editable format, and that's it / period / end of story. Everything else is done in other software. So I don't know if it's the device and/or audiogate that is the root cause (yet). I do know that sox's trim function when pulling content from about an hour in injects drift where there is otherwise no drift. Could just be my current version of sox. Could be my old 32 bit laptop. Could be something in the file formats. Could be many things. Korg can wait until I figure out what it is and what it is NOT.