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Ok, I see. The problem is that some obstacles are not cleared even though they are removed. There is a obstacle height threshold and if the obstacle was detected within this threshold and then was removed, the beams probably hit something (a wall in the background) and therefore are not considered for clearing.

There are few workarounds. First you can try reducing your raytrace range to something close but still greater then the obstacle range (for example if obstacle range is 20, set raytrace to 25-30).
Also, you can try adding the sensor in observation sources twice but this time disable marking and keep clearing enabled. In this case you will have 2 observation sources where one does marking and clearing and the other one does just clearing and you can tinker with the parameters.

There was also an issue on this problem and a commit that fixes the obstacle height calculation.