We are encountering an issue where new code updated within a file is not being found/utilized when that file is updated in an account as part of a bundle install. While the file contents are not accessible on the installed account, the file size changed greatly and the new file size on the installed account matches the file size on the origin account. It appears that the code is somehow being cached from prior to the bundle install. Has anyone else encountered this? If so, any suggestions as to how to knock netsuite back to its senses to recognize the updated code?

Are you sure the scripts are pointing to the right file? If its a client side script, i'd clear your cache and then try again and that is notoriously a problem area.

Assuming this file is uploaded via SDF, try editing (without any changes) in the file in file cabinet and save.