Sometimes issues have been added to the project tree but subsequently disappear from the tree, as if they have been lost. The issues still exist, but cannot be put in the tree again, since R4J thinks they are already part of the tree. The cause of this problem is unknown, but there is a simple solution.
The first solution is available to any user of the project. Right click on any folder in the project tree and select "Add existing issues" then select the source "Move issues within own project tree". You can use a JQL query to indicate the Jira issue that has been lost.
Another solution, which requires your Jira Administrator, is to use the option Check Folder & Issue References in the R4J integrity checker to fix the problem. Unfortunately, this solution does not always succeed, so you might still have to go back to the first solution.