Hmm, normally we do verify success of registration. You can indeed only have one “main” client per number. There’s a draft (very much WIP, not usable yet) to have Whisperfish as “secondary” device instead of primary. That way, you can keep the Android registration and use Whisperfish in parallel.
That said: if Whisperfish says the registration was successful, it definitely was successful. If you have issues afterwards, something else went terribly wrong.
Deleting those directories and re-registering should resolve most things indeed, but that means you lose your messages. Feel free to get in touch to debug whatever is going wrong; I don’t have any troubles myself currently.