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As an update to this, Fastmail confirmed that this was due to a reconfiguration change at their end. I had a similar issue to @akorvemaker on one account in Aquamail and also solved it by wiping the account. The change seems to have involved changing the folder hierarchy, so folders that were sub-folders of Inbox moved to the same level as the Inbox, which then broke a few things. In general, rediscovering the folders in my email clients resolved the problem.
I have since moved the folders back to be sub-folders of Inbox, but this has broken all the custom Seive filters and they way that folders are referenced in Seive seems to have changed so I am now trying to work out how to get mail into the folders again.
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