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I have two inner layers in altium for a flex cable, I want to swap one copper layer with the other without having to delete or copy everything. Is there a way to swap two PCB layers while maintaining everything on that layer?

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The easy way is to just tell the board shop what order you want, or to imply the required order by renaming the Gerber files to indicate the desired order.

I provide a readme.txt file with a board order containing the following (among other information):

The following files are required for this job:
  alarm-Front.GTL   Component side copper photoplot file
  alarm-Back.GBL   Solder side copper photoplot file
  alarm-SilkS-Front.GTO   Component layout silkscreen
  alarm-MASK-Front.GBS   Solder Mask
  alarm.drl   Drill file
  readme.txt    This file
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If they are not top or bottom layer you can use the Design->Layer Stack Manager to move the layers around (and you can rename them to make sense).

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