I uninstalled version 4.01 of the plugin after seeing a number of errors and warnings about graph-indexer (see attached log file).
After uninstall, I archived the %bitbuckethome%\caches\charts-and-graphs folder, then reinstalled the version 4.01 add-on using the manual upload [from url] method.
The url I specified was https://marketplace.atlassian.com/download/apps/1212147/version/100300030 and it installed fine with my activation key already there [from previous install].
The caches\charts-and-graphs folder was automatically re-created and no further indexer errors have been logged.
Let me know if you have any other questions.