As a work around you could try the LV2 version of Dexed. As for the actual problem, it's quite possible the Dexed VST uses chunks to save it's settings. I didn't implement this but as I understand it ...
Dexed VST from DISTRHO-Ports: Dexed VST 0.9.4h from upstream: While I'm not sure what can be done, one option I could see is being able to flip the option per plugin, but something that just work is ...
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