Hi Jerami -
Forgive if you already know this, but something you can do as a preventative measure in the future to save the Aquaero settings is on the Aquaero 5 tab->System page->Settings section click Export Settings. This lets you save all Aquaero settings into a file which can be imported back in if you ever need to. As far as I know, this covers controllers, sensors, etc... basically everything on the Aquaero 5 tab (or at least everything I've messed with so far). This doesn't save any of your overview pages. You need to export them each individually.
As for the other problem: While you're in AS and setting up something - maybe a fan controller - everything works fine? E.g. you can change your fan speeds and what not? You can read sensors?
The
way I understand it, almost all the settings you make in AS on the Aquaero page are actually stored on the Aquaero. So, if you, for example, make a set point controller to run a fan at a certain speed, do you see the fan respond? If so, the fan should keep going if you close AS and reboot your system because the setting has been saved to the hardware itself. Maybe you could give a specific example of a setting that isn't being saved?