Hi there.
Have you tried to check the output of the WooCommerce webhook for both cases? Are the outputs exactly the same?
If there are some differences, you can then set a filter to stop the flow after the webhook for the second trigger.
If the outputs are exactly the same, you can then add the following logic:
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Add a datastore/Google Sheets module at the end of the scenario and map some unique identifier into this database. (some ID, email, etc…)
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Add a search module (datastore or GS) after the webhook module and use its built-in filter to find out whether this record is already present in the database. You need to set up a filter after this search module to stop the flow in case the search module finds a match.
Hope this makes sense and helps.
Cheers,