Hello! Yes, I know what you mean - the Ender 3 doesn't keep the updated settings after you power-off.
The way round this is to have a script in your slicer that sends the commands to the printer every time it starts a print job. I use Simplify3D but I'm sure Cura or other slicers must have an option to use a script.
My start-script contains the following lines: (Yours will be different)
;Set the multipliers for X, Y, Z and Extruder
M92 X80.40 Y80.36 Z403.83 E99.46
;Save them to the printer
It has to do this every time otherwise the printer goes back to factory defaults.
Hope this helps!