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When you do a factory reset, does it fix the issue? Even if the problem shows up again, it's probably easier than manually unregistering WSL distros. It might be a good idea to create a github issue for this.

Do you know if rdctl executes something to register or unregister the distros?

Technically it doesn't - the code that registers/unregisters distros is in the main Rancher Desktop process.

rdctl

just talks to the main Rancher Desktop process. Registering WSL distros happens during Rancher Desktop startup (i.e. when you see the little progress bar in the bottom left part of the Rancher Desktop window). WSL distros are unregistered when a factory reset is done.