Lucene Index vs. Rank Index
As a rule of thumb, whenever you see an ActiveObjectsException, SQLException related to AO, or a RankException, there is no purpose in reindexing JIRA because the problem is not related to the Lucene Index. If something with the Rank Index is broken, it will most likely have to be fixed in the database itself.
In other words, Reindexing Lucene cannot fix Rank Index Exceptions.
Lucene Index:
Lucene is a search engine used by JIRA, and its index contains most (not all) data related to issues in JIRA. Whenever you search for issues in JIRA, the Lucene index is queried. This index can be regenerated, which is useful when it is outdated (for whatever reason).
Rank Index:
The Rank Index is used by JIRA Agile and stores the position of each issue in JIRA relative to each other. The data is stored in Active Objects (AO) tables within the JIRA database, and read into memory on JIRA start-up. This data is NOT generated; therefore, regeneration is NOT an option. Furthermore, it has nothing to do with Lucene, so a Lucene reindex won't fix any problems related to it.