First of all, thank you for writing such a fantastic plugin which saves me hours and hours of work!
I used the bulk rename functionality from within the Media Library page to rename my images. I'm using WP 3.5. This seems to be working (and all my Portfolio posts referring to those images also have their links updated), however, not all database attributes of the image have been updated. In particular, the file name field of the "original"/"fullsize" image as stored in the database is still showing as the old file name, even though the physical files themselves (original size) have been renamed on the server.
This causes some plugins that refer to this field (e.g. Watermarking) to fail.
Sorry it's a little hard to explain but I'm not able to include a screenshot in this support forum. If you could send me an email to Mario@marzuki.co.nz I'll be more than happy to send what actions I took and a screenshot of the final result?
Many thanks again for your help and looking forward to hear from you.