Heads Up: To avoid this error don't define new filenames that contain a dot.

In Bridge Batch Rename, if I choose to use a new filename that has a dot in it (e.g. name1.name2_unique-identifier) then the RAW files lose their extension and the JPEG files are named differently, see typical results below:

For the JPG's: name1.JPG, name1(1).JPG, name1(2).JPG etc.
For the ARW's: name1.name2_unique-identifier etc. i.e. NO ARW extension.

This destroys the association between out of camera RAW and JPG.

REMEDY: With a bit of care the batch rename can be used again (once for the RAW and once for the JPG) to alter the naming, restore the .ARW to (just) the RAW files and restore the association by using the EXIF info. But it's fiddly.