I actually found that my behaviors are stored in application support/remote buddy. I assume I shall need these too for remote buddy to work the same way on a new computer.

When pairing the remote harmony with remote buddy, 10 apple remotes were created. I then mapped these physical remotes with 10 logical remotes I created. 
I assume that as long as I use a new remote harmony which remote buddy treats as 10 apple remotes I can always remap the new apple remotes to the already existing (via the backup of the preferences) 10 logical remotes.