Unless the emulator has a setting to always be in focus (which seems unlikely to me) then no, this can’t be fixed. This is just how computers work. When you have multiple applications open, the one “in focus” - the one you have clicked on - is the one that your key presses or mouse scrolls affect.

It’s like if you have two web browsers open, scrolling the mouse wheel only moves one of the windows, the other one stays unaffected. You can research if the emulator has a setting to always be in focus or if it has a way to respond to global hotkeys of some kind, but you might be better off viewing your notes on say your mobile phone. That way you don’t have to worry about taking the focus away from the emulator.