I encountered this too.

The workaround I used was to edit /etc/etckeeper/etckeeper.conf and add
the following line:

BZR_COMMIT_OPTIONS="--unchanged"

This will give you empty commits in your history, but at least allows
things to work.

-- 
update failure when etckeeper uses bzr and tries to make a no change commit
https://bugs.launchpad.net/bugs/221383
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