Remove from Flow - Do you need two smart lists or combine?

There are a couple of ways to prevent a lead that has registered from being sent a second invitation. 

Perhaps the most straightforward method is to have a second smart campaign for sending the second invitation.  It can be requested from the smart campaign for sending the first invitation.  It would have the following filter in its smart list:

Filter 2 - Member of Program	Member of Program is 'true'
	Program is 'Webinar'
	Progression Status is not 'Webinar > Registered'

You can have a separate listen campaign that says

Trigger: Fills Out Form IS "Form X" on Page "Y"
Flow: Remove from Flow Campaign IS "Other campaign"

As Elliott noted, in this situation you are probably better off with the second Invitation as a separate campaign. Marketo's default Program Webinar template shows it this way I believe.

Campaigns:
-1 - Invitation
-2 - Reminder
-3 - Registration Confirmation
-4 Thank Yous

Definitly agree with the above as a best practice way of not inviting already-registered-leads -> BUT yes, you could remove them from the flow on the smart campaign that sends the thank you email too.