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.pwn file is the source file or your gamemode/filterscript/whatever and the .amx is the file of your compiled gamemode/filterscript and the .amx file is the one that server needs.
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pwn is the source file, it's a simple text file, that you can easily read, understand, and modify.
amx is the binary file, machine code, that your cpu understand.
Try open a amx with notepad: it's not humanly readable.
