The main difference between Cedar Backup version 2 and Cedar Backup version 3 is the targeted Python interpreter. Cedar Backup version 2 was designed for Python 2, while version 3 is a conversion of the original code to Python 3. Other than that, both versions are functionally equivalent. The configuration format is unchanged, and you can mix-and-match masters and clients of different versions in the same backup pool. Both versions will be fully supported until around the time of the Python 2 end-of-life in 2020, but you should plan to migrate sooner than that if possible.
         A major design goal for version 3 was to facilitate easy migration
         testing for users, by making it possible to install version 3 on the
         same server where version 2 was already in use.  A side effect of this
         design choice is that all of the executables, configuration files, and
         logs changed names in version 3.  Where version 2 used
         "cback", version 3 uses "cback3":
         cback3.conf instead of
         cback.conf, cback3.log instead
         of cback.log, etc.
      
So, while migrating from version 2 to version 3 is relatively straightforward, you will have to make some changes manually. You will need to create a new configuration file (or soft link to the old one), modify your cron jobs to use the new executable name, etc. You can migrate one server at a time in your pool with no ill effects, or even incrementally migrate a single server by using version 2 and version 3 on different days of the week or for different parts of the backup.