It took me a long while to figure this one out. My changes were still being seen by VSCode and Gitlens, but they were not being tracked in the gutters... for SOME files. Uninstalling VSCode and re-installing would allow tracking for a bit, but even with all extensions off, it would eventually stop tracking in the gutter.
My solution:
I had renamed a few folders by changing the case. Git was not set to track case-sensitive, my Mac was viewing them as the same file, and VSCode was just being VSCode... Going back and renaming the files through Git ended up fixing the issue:
git mv navigation tmp
git mv tmp Navigation
successfully updated it. If it isn't working, I also had to updated git global (temporarily) and pushed with:
git config --global core.ignoreCase false