Manual update of an app

What happens, if I update an installed app (e.g. Nextcloud) manually?
I expect that the update within Nextcloud will work fine.
But what happens if Yunohost updates the package one day? Will it potentially cause inconsistency/break?

There’s no categorical answer, devil is in the details

Maybe it’ll be fine, but maybe you’ll foget to re-tweak some permission or whichever mechanism such that it matches YunoHost properly etc, and then you end up in intermediary state that Yunohost’s app scripts will not expect. Can really say much without dissecting the entire app scripts and compare it to “what will you do instead”

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My suggestion is never to manually update an app by itself without using the YunoHost’s scripts, you never know the impacts it can have.
BUT, if you want to upgrade, you can upgrade the scripts on git.
It may be quite complicated, depending on the app, but for small upgrades, it should just be a version to change in a configuration file / download link.

For example, here is the pull request for nextcloud 27.0.2 → 27.1.1

Oh, and for many apps, there is also a testing branche, more up-to-date (but that can be risky)