1) When I want to export my Protel DXP file to gerber and an NC drill file then sometimes the output is not readable in an independent gerber viewer like Gerbview, only in Camtastic - which is an Altium product.
It's pretty likely that if Gerbview is properly configured for the format of the Protel-generated gerber files, it will be able to read them.
2) When I change the layers to be exported then often the old layers still can be seen when the Camtastic file is generated. Is this a bug or do I do something wrong?
Not likely a bug, rather, a lack of understanding how to generate plots and work with them with CAMtastic.
I'm not familiar -- yet -- with DXP, so perhaps DXP supposedly integrates CAMtastic so that you automatically see updated files when you generate them. I hadn't heard about that as a feature, however. But see below.
To get a better answer, I'd suggest that you detail exactly what you are doing. What steps are you taking, precisely, that lead you to expect you will see (1) files in Gerbview and (2) new files in CAMtastic?
In P99SE, "export" is a process whereby files that exist in the Document view as part of the .ddb file are written outside that file, as ordinary Windows-accessible files. In 99SE the CAM manager, if properly configured, will automatically export the CAM files as part of its process, since usually you will want to use them outside of Protel. It can do this in various ways. My own system is set up such that it creates a directory with the name of the PCB file and the CAM files, including gerber, are exported there. If I regenerate the files, the earlier versions are overwritten. If I understand what you wrote above, if I disable some layers and enable others for gerber generation, the export directory will now contain all layers that have been generated, so if you point CAMtastic at that directory and command it to automatically load all the files, yes, you will see the previous layers. It's not a bug. Export does not erase any files, it only writes files (which might overwrite any files with the same name.)
CAMtastic is an Altium product, that's true, but it was an independent product until Altium bought the company. So it does function as a confirmation of your Protel output.
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