Using a live website as a base for an existing gitlab repository

Hello Gitlab. Since i’m quite new at this i may or may not have a weird question. After several “ftp hotfixes” the situation is that my live website has the latest code changes which an existing gitlab repository has not. My question is: How do i go about correcting this? In other words i want the code on the live website to replace the code inside the existing repository without losing all the issues in the repository which act as a knowledge base.