The update has to be applied on all servers. You should start with the master server. The updater will ask if it shll update permissions in the master database, you should have to say "y" on one of the servers, it does not matter which one as all permissions get updated for all servers in this case.
As a sidenote: We will release a bugfix version soon which fixes the bugs found in the last two days, so you might want to wait a few days until you update.
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