To the best of my knowledge there is not a way to recover an index from the command line. The REST API for Jira does not have this ability yet. Furthermore, you should not expect to be able to simply replace the files on your filesystem to affect this change.
The documentation in Recovering your index explains that this has to be done by going to the Indexing page in your browser, selecting the file itself, and then click recover on that page. The reason you can't just replace the files directly on the filesystem is because Jira is using a number of different system caching methods. Jira is not expecting those files to be manipulated external to its own processes. By following these steps, it allows the application to know these are changing, and in turn perform a followup check on the indexes and changes since the swap to reconcile any differences.
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