Have you tried already how EV4 behaves in these cases? Your scenario is exactly why we started using the breadcrumbs to extract logbook entries from instead of "stupidly" only monitor the plane speed.
Its for example quite easy to add (maybe that is already, I don't know) a condition that a takeoff is only considered a new flight it its at least 10 minutes after the last landing.
For FI's the option menu->system->[Location updates even when app in background] (turn it on) together with [location updates only when in flightmode] (turn it off, so EV4 tries to record as much as possible in the daily breadcrumb) is a nice experiment maybe.
At the end of the day (or and convenient moments during the day) simply select the daily breadcrumb in the menu-> [Flightlog maintenance] ->Daily breadcrumbs and have EV4 [Extract logbook entries] from it. If you collect a few daily breadcrumbs the upcoming time we can try to improve this logbook creating.