When you use the Assign menu to configure your footswitches or encoder, the changes you make will only take effect for the loop you are currently using.
If you do not overwrite the loop save data with your updated Assign settings, the changes you make will not be remembered.
As you load a saved loop, the loop audio along with it's Assign settings will be loaded together.
The Assign settings are not global and are unique to the loop you are using, so please ensure that each time you change your Assign settings, your loop save file is overwritten.