Thunderbird runs filtering on all the email together only after all are downloaded. We have to look at all the unwanted emails listed in the inbox until all downloading is complete.
Instead, it should apply filter on each email as soon as it is downloaded, before the next email is downloaded, before listing in the inbox, so we only look at the good ones in the inbox.
Sometimes we are waiting to see a specific sender's email, but it gets mixed with others, then have to wait until all the download is complete for filter to apply.
It is obvious in pop3.
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I have not had mail that is to be moved by a filter remain in the inbox more than a few seconds after the download completes. In support, I am always trying to find ways to ensure the download is complete, like setting after junk classification to ensure filters actually work correctly. I really think trying to filter mail as soon as it appears in the list is doomed as only the list display stuff for that mail is actually downloaded at that point in most cases.