If you have PS CC:
Add a new action to the existing set, that contains a single step that renames the Background layer, to "Layer 1".
Then insert a conditional step at the beginning of your core action (to do so, click the actions panel menu button, and select "Insert Conditional"). Then:
- Choose the condition "Layer is Background" from the "If Current" menu.
- Select your new little action from the "Then Play Action" menu.
- Leave the "None" option, in the "Else Play Action" menu
If you have PS CS6 or older:
Insert the Flatten Image command at the beginning of your action. Then edit the action so that it starts from the Background layer.
Set up the action same as you are now, except use:
- Alt/Opt + [ or ] to move back/forward one layer
- Alt/Opt + Shift + [ or ] to add one layer back/forward to the active selection
- Ctrl/Cmd + [ or ] to move a layer down or up one
This will take any layer name referencing out of the equation, and replace it with "move active selection/layer by one"
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In my frequency separation action, I used a layer set and an explicitly named layer, so it does not matter if the original is a flattened image or if it has one or more layers as this is creating a non destructive copy and is not dependent on the original layer names/structure.