Some animals use shells as a sort of refuge to protect themselves. Is there a particular verb for it? I am not sure if I ever heard of such a word, but there must be a word for it or at least a better way to say it than "take refuge in a shell", because it's too long-winded.
You could use hide and still convey the same meaning.
to conceal for shelter or protection. E.g. They hid him from the police.
So in your case, it would be Some animals hide in their shell
Retreat is a possible option: Some animals retreat into their shells when in danger
an act or process of withdrawing especially from what is difficult, dangerous, or disagreeable