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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>