Hi Jayke (@schnooks)
This sounds like a problem that an SCM tool like git could help you with.
You’d probably want to keep your code in a private repository which will cost you a little bit of money. I believe Atlassian BitBucket still lets you have private repos for free.
There are many options in terms of how your theme update / development workflow might look. You could have multiple repos or use multiple branches and manage changes through pull (or merge) requests between them.
The advantage you’d have is the ability to see what the update is changing, detection of conflicts between theme updates and your custom changes and history that you can undo or revert back to.
Maybe others in the community have a workflow that works well for them? Or you could share your journey to custom theme nirvana?
If you’re new to Git and version control here’s a few articles that might help you get started and maybe get you as confused as I was starting out with Git: