Currently enabling aerc in accounts.email.accounts.<account> doesn't handle existing configs where accounts.email.accounts.<account>.notmuch.enable is set to true. This pr proposes to automatically set notmuch as backend for aerc if this is the case, see rjarry/aerc@master/doc/aerc-notmuch.5.scd.
For set-ups where accounts.email.notmuch.enable has been enabled this was previously ignored, so this is probably a breaking change for these configs, but from running this set up during the last weeks I would consider the upside of better search and filtering performance as significantly larger than the minor changes in query handling as noted here rjarry/aerc@master/doc/aerc-notmuch.5.scd#usage.