The linked assembly should not be part of the Dotfuscator project, but it should be readable by Dotfuscator. I suspect the referenced assembly is in the same directory as your input assemblies on your workstation, on the way to your workstation or in the GAC. The referenced assembly is probably not located on your build server (or Dotfuscator cannot be found). You can provide Custom assembly loading paths where Dotfuscator will additionally search when trying to resolve referenced assemblies.
A linked assembly is required on the assembly server for Dotfuscator to successfully obfuscate, and the best way is to either ensure that the referenced assembly is in the same directory as the input assemblies, or to use the load path of the custom assembly.
In addition, new in version 4.5.1200, you can first find your user-defined download path, and not the default for searching the latter.
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