Hi librandi
It seems that you put the custom css into the a file in theme folder:
/templates/ja_mono/css/themes/orange/custom.css
The only place for custom.css file is in: /templates/ja_mono/css/
Or another place to override css is the css file in local folder of template:
/templates/ja_mono/local/acm/clients/css/themes/orange/style.css
These 2 places will not be affected when you update new version of template
Regards