As the CloverETL Designer is basically an Eclipse plugin, the TLS should be enabled in a similar manner. Please try to add the following VM argument to the run configuration of your graph(s).
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You can add the VM argument via the Designer's top menu -> Run -> Run Configurations -> <your_graph> -> Arguments.
You should also consider upgrading your CloverETL Designer as version 3.5 is obsolete and there were some TLS related changes made since then.
Hope this helps,