Kivy does (sadly) also take/set the root logger, we hope to change that, but we have to evaluate if that would cause issues.
If you can still import PyUpdater as long as you import it before Kivy, then you can decide to import it in your main module (before kivy), even if you don't use it there, as python modules are singletons (importing them in another place of the same running program gives you access to the same namespace, that is global to the application), that would allow you to import it safely later in another module.
import pyupdater # noqa
import kivy
...
in another module
import pyupdater
should now work.
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