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This seems like mininet issue as suggested above. L2switch is just reacting to an event received from switch that the link/port is down. Link removal would happen only in case of loops ideally.

Other possibility is loss of lldp flow issue. Things to check is if the s1, s2, s3 still have the original lldp flows installed then the controller code is not initiating this link drop. It could be mininet which is running out of resources at that time?

This is just a thought based on information provided.