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Thanks for asking.
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