In general, if you see any kind of symptoms that your Jira index is corrupted (for example, your JQL queries will return wrong data), then disable BigPicture, perform Jira re-index, and enable BigPicture back.

Work breakdown structure data is stored in the BigPicture table called:

 WBS_NODES
CODE

If you have a backup that contains such a table, your WBS can be restored.

Maintaining a Jira index is critical - when the index is corrupted, synchronizing tasks can result in data loss (existing task hierarchy is changed). When index it is corrupted, JQL does not work and the plugins treat all the issues as new during the synchronization; this means that the task structure based on artificial tasks is changed during a sync. Old structure is lost. 

More about Jira index corruption can be found in Atlassian documentation:

Impact on synchronization

Full synchronization is not run when BigPicture gets information about the corrupted index from Jira API. A user can perform a Jira re-index; this should solve the corrupted index problem. Users can also continue without reindexing, which can cause irreversible and unintended changes in Box scope.