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Sorry for the late reply, for some reason I did not get an email notifying me of the update / comment...
There is an experimental feature to incrementally update the 2D projected map, instead of regenerating all of it. This may be the culprit since it's not completely tested. However, the default for the parameter ~incremental_2D_projection
should be false, did you enable it?
There should be a debug output "Rebuilding complete 2D map" for octomap_server, in that case mapUpdateBBX... is not used.