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I need to publish a workspace into FME Server that has a disabled connector and disabled transformer. In FME Desktop 2021, the workspace can run successfully with these disabled. If I publish this workspace to FME Server 2021 and create/run an Automation, will FME Server recognize the disabled connector and transformer and not run them?

Yes, FME Flow (Server) will recognise you have disabled transformers/connections

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