Problem when copying a theme and using LESS

So I have a theme I use as a template for different sites. I recently started using LESS, compiling it locally and uploading the compiled style.css to my WordPress.

So I will edit my template to how I want it and then I’ll make a .zip of that theme and install it for my new website. Everything will be fine until I edit some .less and compile a new style.css for my new website. It seems to lose all of my custom CSS.

Please let me know if I can provide anything else to help.

Thanks!