After the latest upgrade (12/17), several customers are reporting this misbehavior:

Automated message: Errors were encountered while processing smart commits
Due to the following errors, the smart commits were not actioned and will need to be performed manually.
Error processing NG-229 #time 15m
FishEye was unable to log '15m' against the issue NG-229. There is no mapped project "NG" for repository "NG".
See the documentation for how to invoke JIRA Issue Transitions automatically.

It seems that the JIRA app links are no longer available.

I have upgraded my own JIRA-DEV instance from fireball-190 to fireball-192 and confirm that it removes the app link from Fisheye.

• EDIT *
  This is also caused by https://sdog.jira.com/browse/ODC-76.
  Note that not all customers with FishEye are affected as there is a race condition.