How to Target by Unique Identifier with Duplicates

Hi everyone,

I recently inherited the Marketo instance at my company and have questions on how I can target by unique identifier in a situation where we utilize duplicates. Our unique identifier is email address and program, so one email address can have multiple records associated with several different programs. Additionally, when a record submits an apply now form, a new lead is created in SFDC and synced to Marketo. These apply now leads are routed very differently and assigned to non-marketing queues. I am trying to automate a campaign that targets these duplicate self apply records by unique identifier or email address in order to remove from a nurture flow, but because different SFDC record IDs are members of different smart lists/campaigns, I am running into difficulties in targeting them. Here is the outline:

smart lists

A -  New Self Apply Leads and duplicate fields = email address 

B - Member of Nurture and duplicate fields = email address

smart campaign

if member of smart lists in both (A and B) and duplicate fields = email address (Two separate records that cannot qualify for both)

flow - mark cadence as paused

My goal and thought process is if an email address is going through our nurture program and then progresses to a new self apply lead, we definitely do not want to keep emailing and encouraging them to start an application! I understand what I've got so far is messy due to the way we are handling the self apply leads and because the records in smart lists A vs B have the history of separate records on their log, and therefore not triggering the regular pause nurture campaign. So unfortunately I cant write the logic like "member of smart list A and opened email was from the nurture". Worst case scenario is I have to use vlookup from exports and manually remove, but looking for any advice on this, thank you!