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You could add a step in your sync campaign that checks if the lead is part of this list and if so, it removes from flow, before the sync flow step.
It would look like this:
Lead is created (assuming this is what you trigger on)
- if member of list (list you want to suppress) --> remove from flow
- sync (and insert the rest of the flow actions here)
You could also use a choice on the sync flow step:
- choice1: if member of list --> (leave empty, ie, do nothing)
- default: sync
Alex is right, you can remove records prior to the sync to SFDC flow step, but be aware that if the Mkto program is synched to a SFDC campaign, then the records will be synched anyways if you update their program status. There are other flow steps that create an implied sync and the records get into SFDC, like change owner, create a task, etc. Check out this doc for more info: Implied Salesforce Actions - Marketo Docs - Product Docs
Also, I would caution this approach of changing the emails in SFDC later. Once you update them in SFDC, you will need to merge them all 1 by 1 with your newly created Mkto leads so that all activities are associated with one record. Depending on the size of the list, this can be quite time consuming.