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I ended up searching alternative to native tf library functions to solve my problem. The reason was that after getting allFramesAsYAML() (or in Python tfBuffer_ros.all_frames_as_yaml()) to work i found out that it will return _all_ frames that have been in the tf buffer, regardless of whether the frame is in the current tf topic or not. The output was:

marker1: 
  parent: 'camera'
  broadcaster: '/marker_tracker'
  rate: 30.401
  most_recent_transform: 1585572193.003
  oldest_transform: 1585572190.503
  buffer_length: 2.500
marker2: 
  parent: 'camera'
  broadcaster: '/marker_tracker'
  rate: 30.457
  most_recent_transform: 1585572192.703
  oldest_transform: 1585572190.503
  buffer_length: 2.200
marker3: 
  parent: 'camera'
  broadcaster: '/marker_tracker'
  rate: 27.709
  most_recent_transform: 1585572195.538
  oldest_transform: 1585572191.568
  buffer_length: 3.970

I occluded marker2 after a while, and it still appeared in the output. The only difference is that "most_recent_transform" stopped updating.