In case you have a custom developed node, you have access to the RED object which contains the server (RED.server). So you could implement certificate updates there... The RED object also holds the settings.
You could even create a simple custom node just for that purpose - Such a node wouldn't even have to be part of any flow, you could enable the functionality when the node gets added to the pallet. You would obviously have to be careful that the node would be implemented as a "singleton".
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