There's no magic solution for this as applying the picture changes to your audio tracks will always require fixes. For example, if in the vision edit a bunch of shots are swapped during a music montage and the music isn't changed, applying the picture changes to your Pro Tools tracks will cut your tracks when they didn't need to be. The other example is in the vision edit they may have made some changes to audio clips only, like changed a couple of voice-over takes. These changes will never come across in a picture change list. Hence these extra fixes always need to be made after an automated re-conform is performed.
However saying this, generally apply the picture changes to your audio tracks gets most of the work done that you would need to do. Once the changes are applied with an application the holes and edits need to be fixed and then you'd need to play down your edit tracks and compare them with the guide tracks of the new pictures to make sure they match.
Also, as mentioned above, this process relies on getting good data from the picture editor(s) and setting up a work-flow to handle these changes in an efficient way.
Another application to check out is EdiLoad. It not only re-conforms Pro Tools tracks for picture changes but can also conform (assemble) your location WAV files in conjunction with the Pro Tools expand tracks feature. It can also export a text file listing picture changes so you can update your session manually by inserting and deleting the required frames at a location that works with the material in your tracks.
http://www.soundsinsync.com/products/ediload
Regards,
Mark