How Lightning Networks protect itself from 'Selfish Mining'?
Your question seems very similar to the 51% attack vector on the lightning network which I described on the lightning dev mailing list. I am not aware of any protocol to prevent this nor do I see any way of preventing what you and what the mailinglist post describe. The timeouts depend on blockheight and the Bitcoin protocol has the consensus rules that the longest proof of work chain wins. 

I think it is a generally accepted assumption that Bitcoin will only operate in a secure way if at least 51% of the mining power comes from honest nodes (which are following the rules) on the plus side any secrete mining operation would statistically speaking only be harmful if the operation has at least 51 percent which is hard to achieve and probably also more expensive than the gains from winning such an attack.