Ok, that error is almost certainly the cause of the issue. If possible, you should re-index as Joe said (no need to delete stuff - in fact, a simple edit of the issue affected should fix the problem for that issue. Obviously though, for deleted issues, you'll need to do a full re-index. This would be an excellent test as well)
The root cause though, is that you have a broken plugin. I'm guessing the usetfs string in the class name means it's related to some form of TFS integration. Check the versions of any TFS related plugins you have, disable the ones that are not valid for your versions, or look for upgrades.
2013-06-05 12:58:34,952 QuartzWorker-0 ERROR ServiceRunner com.pigsty.jira.plugins.usetfs.revision.RevisionIndexer:job [sal.jira.scheduling.JiraPluginSchedulerService] Unable to load a service descriptor for the job 'com.pigsty.jira.plugins.usetfs.revision.RevisionIndexer:job'. This is usually the result of an obsolete service that can removed in the Administration section.
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I think the first course of action would be to try a full re-index. If possible, please perform a full re-index from scratch. To do so, follow these steps :
Also, if you are using JIRA 5.2 or above, please note that it's generally better to use the 'Lock JIRA and rebuild index' option. Although it would lock your JIRA (no one would be able to do anything), but it can be more effective
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Sounds like the index was not updated correctly.
How did you delete the issue? Are there any errors in your logs around the time of deletion? Is it possible to schedule a re-index?
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2013-06-05 12:58:34,952 QuartzWorker-0 ERROR ServiceRunner com.pigsty.jira.plugins.usetfs.revision.RevisionIndexer:job [sal.jira.scheduling.JiraPluginSchedulerService] Unable to load a service descriptor for the job 'com.pigsty.jira.plugins.usetfs.revision.RevisionIndexer:job'. This is usually the result of an obsolete service that can removed in the Administration section.
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first thought of it would indexes in JIRA was not updated. Try to reindex as it would rebuild the indexes again. However, the JIRA instance will be inaccessible during the indexing process running.
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