Unfortunately there is no out of the box solution for this.
You could try to have a 'flag' inside your data that would show which is CB and which is classic, like a row in the sendable DE that is collected in Send Log (may not work if your sendable DE goes out to classic and CB emails).
Or you could set an AMPscript var in each email that identifies which builder you used and have that collected in the Send Log. E.g. create a column in the sendlog named 'Environment' then in each email put in
SET @Environment = "CB" (or "Classic" on Classic emails). You can then use this field to differentiate your API calls in for SOAP or REST.
Another solution is you could put a flag inside the naming convention on your emails, so that if CB the name would prefix with 'CB_'. You can then utilize the email name to differentiate on your data collection.
If utilizing a flag is not an option, your only other option then is to use a REST GET with a filter on email objects only to collect name/id combos of all the CB emails and use REST retrieves on them and then exclude those emails from your SOAP calls. This can be unwieldy and process heavy though.