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If your ADS layers are the same as the GDSII layers, you can also use "Automap" instead of the layer mapping file. This will create a 1:1 mapping with the same layer number in ADS and GDSII. A custom layer mapping file is only needed if you want other layer mappings, e.g. skip some layers on import or map to different layer number.
The problem I encountered id : when I export .gds file and layer map file and i save substrate file, i compared information on those files. I found that layer number on substrate file is different than layer number on gds and .map file
You should get the numbers that you defined yourself.
Can you show screenshots what numbers you see where (ADS layer #, GDSII layer mapping file, substrate file) and explain why you think there is an issue?