Filing shared email messages without removing from others inboxes

I have several email addresses and I view incoming messages using the All inboxes favorite. I have two addresses that are shared with others. To keep my inboxes uncluttered I like to remove mail from my inboxes and file in a separate, topical folder. But if I understand the workings of IMAP correctly, once I have removed a message from my inbox it is also removed from the inboxes of those with whom I share the address. So in order to leave these shared messages available to others I am left with them in my inbox, un-filed, and visible whenever I view All inboxes. Any thoughts on how to deal with this? (One workaround might be the ability to remove the inboxes for the two shared addresses from All inboxes, so that the shared messages do not appear when I view All inboxes. That would leave the messages "filed" in my inbox, not ideal, but at least would not clutter up the All inboxes favorite. But I do not see that option. Any other thoughts?)

[Re-Titled by Moderator]