The functionality to remove cached messages from the device was removed.
I don't think it's a great user experience having to manually remove
messages. I have plans to automatically remove cached messages in a way
so K-9 Mail is not using more storage than necessary, but users don't
have to constantly re-download messages they're interested in.
For now you could set 'Account settings > Fetching mail > Local folder
size' to a low value and then manually sync the folders that have a lot
of messages you don't need on the device. Afterwards change 'Local
folder size' back to the original value.