When you first install 2.0 or higher the plugin will scan all folders, jobs and Runs for IDs and will move them out into a side file along side the items configuration. (
*What the plugin migration does not do is validate that the IDs are still unique* (if you previously copied a job for example you will have duplicated). Therefor post migration if you really do require uniqueness you will need to manually inspect these files for duplicates. This is not performed by default as it can give a false sense of security as jobs may have been copied across different masters.
If you find duplicates - then all you need to do is to remove the
unique-id.txt files and a new id will be generated when next requested.
*If you copy folders manually then you will need to ensure that you remove any
unique-id.txt files that are present in the destination after the copy.*