If you reduce the tempo of the audio file by say 20% does Reaper still maintain the correct bar numbering automatically?
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Yes and no, depending on how you configure Reaper in "Project Setting", which allows the bars to be set by Beat or by Time. I generally use "time".
Now that I better understand what you are doing, here are the details about how this is handled in Reaper. Ya, it can be complicated. But it does work well.
https://www.youtube.com/watch?v=A4M4BoYcwPcThis issue goes beyound just setting the starting bar to what ever bar number you like. It has to do with how the project adjusts the "item" during tempo changes.
Or have I just sent us down a rabbit hole??