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Qlik Enterprise Manager is your command center to configure, execute and monitor Qlik Replicate replication and transformation tasks across the enterprise.
So far I know you don't need to uninstall them, in fact you have to keep them installed as the apps that use those connectors needs them to work (they will have a "from url:5555" or like that to use web connector").
New apps or if you modify your apps to use the included web connectors or standar connectors so in the future you can avoid the use of manually installed web connectors.