Archive a message from the inbox and it looses the inbox label. If no other label has been assigned (by filter or user) it is only representatived in "all mail". Very easy to do given Gmail UX which favors archiving.
But you already know that so we are coming at this from different vantage points.
As Kostya pointed out you are responding to something completely different from my point(s).
I wrote:
Unless you intentionally delete or archive a message in your server-side filters, how could it happen that a message would "loose all labels, including "inbox" "?
I do use Gmail, and more than one Gmail account, but quite possibly less than you do. Obviously, our workflows are different. But it looks like you are considering making some changes to your established procedures (you've asked about abandoning "Sent"). In that case, - you might want to consider and read the view that I have on these folders.
I consider "All Mail" label as an "archive". (Which is actually in line with Gmail's procedures.)
I've already written what "archive" means to me:
"Archived" means something that you do not access on everyday basis. You do that once in a while, and then you don't necessarily expect it to have all the same behavior.
So, in that view, - "All Mail" is essentially where
deleted messages "live after death" within Gmail (for me). You can occasionally go there if you need to retrieve from long time ago. (I've never had to do that so far.) So, "All Mail" is not synced in IMAP clients.
All other messages live either in their respective folders (labels), where they get sorted either automatically or moved by hand, or in Inbox, if they do not belong to any major topic. Sent messages live in either "Sent" or in the specific folder where they got moved to.
In this case, you'd have no duplications, no duplications.
(And from what I can tell, this procedure would not create any
additional problems with your multiple labels vs. Aquamail.)
From what I can tell, not actively using "All Mail" folder/label is a very frequent model of Gmail, at least by people who use Gmail via IMAP client (e.g. Thunderbird). And I don't go to "All Mail" even the web-interface, or in Gmail app that I am using for one of my Gmail accounts.
BTW, @Kostya: it looks like Thunderbird is aware of multiple labels in Gmail, and doesn't store message duplicates. At least that's what I read in some online pages at mozilla.org.