You are taking bigger steps for a simple sync.
In general, when you make a config sync from Active to Standby, you would require to do,
(Active)(/Common)(tmos) run cm config-sync to-group device-group-failover
When this is run, the Active configuration gets saved onto the specified device group.
In the event the standby configuration has the latest, it would tell you that standby is having the latest config and would requires to do from B to A. But you would know that Standby might have the latest, in this event, either you can do a force overwrite or make a dummpypool in the Active and then give the above command. This indicates the HA pair, that latest configuration changes has happened in the Active LTM.
Also its not advisable to copy a bigip.conf file of one box and load it on another box. There would be some parameters like bind-pwd which would differ.