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You can use the tf_remap script to filter the output of your bag file. See the tf wiki page

To use it you will want to remap your playback to put /tf onto /old_tf and then use tf_remap to move most things from /old_tf to /tf with your remappings applied.

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matching updated question

You can use the tf_remap script to filter the output of your bag file. See the tf wiki page

To use it you will want to remap your playback to put /tf onto /old_tf and then use tf_remap to move most things from /old_tf to /tf with your remappings applied.

To deal with the timing issue you should set use_sim_time parameter and playback the bag file with the clock option enabled.