I have also found this to be a problem but another big part of this is when I re-activate it after adding new menu items, some of my last menu items get deleted (always at the end). So I deactivate it again, add those deleted menu items back, re-activate it and then it’s fine.
Here’s a good helpful hint on that. Anything after 75 menu items gets deleted. We have sub/sub/sub menus and so it doesn’t seem that many but that is the issue. Anything after 75 gets deleted once we re-activate the plugin.
