To save data all you do is flash the system, you'll still have to disable apps and stuff but won't have to start from scratch like you do when you do a full wipe.
I think I screwed something up along the way, because System Update now force closes whenever I try to open it. So I tried to reflash just the system, but it didn't restore the apps I had disabled either in settings or via ADB. I followed by reflashing everything excluding userdata, but again had the same result. It sounds like a factory reset would be the only way to restore these apps. Unless you know of another way?
Edit: Never mind. I found an apk of Advanced Logging on apkmirror and reinstalling it did not solve my problem. I guess I'm factory resetting yet again...
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