Upgrading opencart theme journal 2 to journal 3

Question

I am new to opencart. I want to upgrade my opencart from journal 2 to journal 3 but I have made some changes in theme files. My first question is: Will my theme files will be replaced? I added code for the admin panel using vqmod and in modification. I saved code from modification to original controllers but what about theme files. Is there any way to keep save the theme code and use it in journal 3? I am using opencart version 2.3.x Thanks