There is an widget you can use to create different styling for different users / organizations. See here: https://appstore.home.mendix.com/link/app/3067/TimeSeries/StyleSheetSwitcher
I use it all the time in multi tenant environments.
My advise would be to create a new theme from scratch (use https://ux.mendix.com/ to create a basic theme) and then inspect your old theme and adjust the new theme accordingly.
Regards,
Ronald