Regarding backup / replication of your settings, instructions are available in the FAQ under: 
http://www.iospirit.com/support/faqs/remotebuddy/category/8/Configuration/

Regarding your Harmony question: 
1) From Remote Buddy's side: the IR codes themselves won't change, so Remote Buddy will just recognize it as previously.

2) From Logitech's side: it depends: 
a) if you replace your remote with the same model: nothing should change.

b) if you replace your remote with another model that uses the same configuration software: your settings are - mostly - transferred by Logitech's software. Detail settings may be lost, though.

c) if you replace your remote with another model that uses a different configuration software (when f.ex. switching to a Harmony 300, which uses myharmony.com): you may or may not be able to transfer your settings. This is something I haven't tried, yet and thus can't share any personal experience.

Best regards, 
Felix Schwarz