For those of you who have SSH access, I've created a bash script.
You'll need your database name, database user, and database password.
Unzip this file, edit the file to replace the database name (without quotes), username (with quotes) and password (with quotes)
Upload it to a directory and run ./compact2dynamic.sh
delete the file when it is finished.
Some tables will take a significant amount of time to complete. My Search Index table took 20 minutes.
After it is complete, run an Optimize Table on all tables (I use phpMyAdmin for this) and all should be well.
This script worked just fine on my setup and removed the warning in the control panel about the compact row types. As always Caviar Empty... or whatever.
compact2dynamic.zip