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We managed to generate gerber files. Unfortunately Altium gives a notification that they are not fully closed.

If you ever receive a message from a 3rd party software stating issues with Polygon export (in gerber files), please try checking the option "Optimize / Fix Polygons".

Important:  "Optimize/Fix Polygons" will modify the outputted Gerber files. -  Unless you are familiar with the behavior of this option, or have 3rd party tools that cannot handle polygons (like Altium); it is recommended to verify the final gerber results or leave this feature unchecked.

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