My name is Tim Zook, I'm the lead developer for MyBookTable.
You're correct that there are some backwards incompatible changes in MyBookTable 3.0. While we realized that this will require a some amount of work to update for some of our users, it was impossible for us to make the new version 100% backwards compatible due to the new Display Mode system and Section Sorting system in 3.0 that affects how book templates are handled, so we decided to make some general cleanup changes at the same time. Since it was a major point release from 2.0 -> 3.0, this was the correct time to make these changes. The templates are now in a much more stable state and should not change in the foreseeable future.
However we'd like to do whatever we can to make this transition as easy as possible, and we'd be happy to provide you with personalized advice and code in order to help get your templates updated. If you can provide us with the details of your template situation (the easiest way would probably be simply sending us a zipped copy of the MyBookTable templates in your theme folder) we can create detailed instructions to get you updated that won't take you more than a few minutes of your time.