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the only way the GTW integration is supposed to work is when you use a Marketo form to register people and mark them with a registered program member status when they do so. The opposite, i.e. registering people in GTW and having them show up as registered in Marketo does not work and the integration doc is clear about this. They will flow to Marketo once they are marked in GTW as attended (if they attend of course).
The right way to use the GTW integration (and other webinar integrations, BTW) is to manage everything in Marketo and deactivate forms and all emails in GTW. Use only Marketo email for invitations, registration confirmation or reminders.
You are right, the only way to fix it know is to export the list from GTW, then delete the registrants in GTW (otherwise you will have duplicates in GTW), then import the list in Marketo and set them as program members with a "registered" status in Marketo. Make sure prior to this that your channel is a webinar type of channel and is set up correctly. Once they are imported in Marketo and mark as registered, they will be pushed again in GTW and it will work correctly.
Thanks Greg, I had hoped this wouldn't be the case! Luckily I only have a few webinars on the old system, all new ones going forward will be via Marketo so I should only have to fix this one time...