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On Windows open C:\Program Files\ArcGIS\Server\bin\ServerTypesExt.dat and remove any references to it :
<ExtensionType file="mysoe.soe">
<Name>MySOE</Name>
<DisplayName>MySOE</DisplayName>
<CLSID>my.soe</CLSID>
<Description>MySOE description</Description>
<MaxUploadFileSize>-1</MaxUploadFileSize>
<AllowedUploadFileTypes/>
<Properties/>
<Info>
<DefaultWebCapabilities/>
<AllWebCapabilities/>
<hasManagerPropertiesConfigurationPane>false</hasManagerPropertiesConfigurationPane>
<SupportsSOAP>false</SupportsSOAP>
<SupportsREST>true</SupportsREST>
</Info>
<Resources>
<WSDL/>
</Resources>
</ExtensionType>