I have had a couple of reports from users who have lost their 'Content\Routes' folder after using StoreThem. I have not been able to replicate this and it does not happen under correct operation of the program, but somehow they have managed to delete the Routes folder while it still held their routes before they had been moved to the StoreC\Routes folder.
This new version includes code to stop any folder being deleted if it still includes sub-folders, so just in case make sure you use the new version.
Also make sure you have backups of Assets and Content in any case, even if you don't use StoreThem, it is better to be safe than sorry.
Mike