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Originally Posted by Kalcor If updating from an existing 0.3x server: you can update simply by replacing the 'samp03svr' file on linux, or 'samp-server.exe' file on Windows, found in the 0.3x server download package.

There really shouldn't be any issues. You don't need to replace anything other than samp03svr. Have you tried the methods for starting on a Linux server?