Encountered a failing job this morning where the logs indicate that a build-dir/_git-repositories-cache subdirectory doesn't exist. Official advice is this:
https://confluence.atlassian.com/bamkb/git-cache-removal-in-bamboo-329982070.html
Basically, use the UI to clear the repository's cache. I tried this: same result.
Looking a little higher in the logs, I noticed that the error cropped up when trying to execute webpack from the job's working directory. On a hunch, I deleted that working directory manually; this resolved the error.
My conclusion here is that the working directory for a job also caches some information. If you're running into this problem, see if removing or cleaning the job's directory (something like %BAMBOO_HOME%/local-working-dir/[PROJECT SHORTCODE AND JOB CODE]) solves it for you. If so, enabling "Force Clean Build" may prevent it in the future, at the expense of longer build times.
