Sieve filters can create duplicates even if you don't run them against the Sent folder because it appears it runs on outgoing messages. It took me a minute to figure out how to stop this, but in the interim duplicates were created, meaning I had the message in the Sent folder, but I also had it in a filtered folder.

So, I went about to delete the message from the filtered folder and confirmed that the original message remained in the Sent folder. All appeared to be good.

I then deleted the "duplicate" from the Trash folder and it removed ALL copies, including the Sent folder.

Now, I'm sure this might make sense to a more experienced Proton user, but it is confusing, to say the least.

I also get that Sieve filtering is advanced, but there should be a way to remove the message from the filtered folder, which is essence deleting what I call the "duplicate".