If your notes appear on LDS.org and/or on other devices, they're safely synced, and they won't be lost by deleting the app.
When you're signed in to Gospel Library with your LDS Account – syncing your annotations – the "master copy" of everything is stored on the Church's servers, and also backed up periodically. What's on your devices is just a copy. When you add or delete annotations using the buttons and menus in the app, the app sends those changes to the Church servers, and from the Church servers, it syncs back down to any other devices.
Deleting the app is different. Because you're not using the buttons and menus in the app to add or delete annotations, the app doesn't know that anything changed, so it won't try to send changes to the server. (In fact, even if Gospel Library wanted to contact the server, it couldn't, because the app no longer exists.

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As long as your annotations show up on LDS.org and/or other devices, then deleting the app is perfectly safe.