I deleted it. A couple hours later (and after reloading Emacs), the same error happened, with the same file name, i.e. I deleted that cache file and it seems to have been rewritten to.
I have already disabled undo-tree-enable-undo-in-region which I hear is buggy.
I have added (toggle-debug-on-error) to my config, but I get no backtrace before/after the error message appears. Any suggestions on how to find the source of this error?