Hi belex24
When you enable from backend Template manager general tab the css optimization then all your css files are stored in the t3-assets folder - that is a temp folder used for this purpose -
When you are working on your website you should first disable css optimization and then apply changes to your css files - ( like custom.css) only when you completed all your customizations you can enable again the css optimization.
Everything about this and rules is explained in the documentation page HERE
Regards