One way to stop your Fortnite settings from being reset every time you load your game is because your gameusersettings.ini file is for some reason set to read only.
This normally occurs if you have made your file read only because you disabled the mouse acceleration option.
To change the file from read only you should, right click on the gameusersettings.ini and select properties. On the box that opens at the bottom will be a read only tick box. Make sure this is unticked and select apply and then ok.
If this doesn’t solve your problem, then I would suggest doing a full reinstall of the game. Although this isn’t ideal there is obviously some sort of mismatch in your files. So, a full reinstall will fix this problem.