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Synchronize the layers, so they all become the standard colors and gerber file extensions ( gts, gto, gtl etc.) that I prefer. Not the .pho which it currently does.

To modify the layer names generated by Synchronize Layers, please perform the following: 
  1. Go to menu:  Setup | Synchronize Options... 
  2. Here you can assign layer colors, and layer names to be used after running "Synchronize Layers". 

Now whenever you use the command Synchronize Layers (menu:  Setup | Synchronize Layers...) those Gerber names and colors will be used.

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