Applying mail app filters only to inbox/incoming messages not archive folder

I've recently moved over to MacOS from Windows and am really struggling with the way the mail app filters work.

I get several hundred emails a day and have set up a series of filters to sort them. This seemed to work fine to start with, but as soon as I also moved my archive of emails and curated subfolders I wanted to keep, some dating back years, the app started to apply filters to this folder of, already sorted, emails too. I just want the filters to work on the incoming emails/those in the inbox, I don't want it to start moving those in my archive around. Is there any way to stop it doing this as It makes the app unusable for me and the alternatives I have looked at either don't support filters or have a default layout that you can't change? The only one that seems to work is Thunderbird, but it keeps making me resubscribe to the imap folders every few days and doesn't appear to sync deleted items correctly as they keep reappearing. It has taken me hours to get my archive resorted, but would like to go back to the mail app if possible as it works fine on my phone/iPad.