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When you drop a bunch of clips onto track 1 and a large wav file for example on to track 2, PD will put each clip on it's own track, cascading them down like a waterfall until the end. Is it at all possible to keep them all on track 1 and 2 instead of manually having to move them all? It would save me a lot of time.
No, and there's no way to change that.
I assume from your description that you have one long clip and a bunch of secondary clips that will sync to it at various points, but PD has no way of knowing that upfront, so it automatically creates as many new tracks as the number of clips you've selected to sync and lays them out as they're synced.
I know it's a pain to scroll way down to retrieve the final synced clips, so it might be a little easier if you only sync 2 or 3 clips at a time, even though that'll be more steps.
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