Thomas is presenting the contrast between what would usually be expected and what will happen at the end of time.
Reason would assert that if someone should "go mad" in the sense of losing their ability to think and act rationally, that person would be in grave danger of losing his/her life. If a person should "sink through the sea" and drown, that would mean that life has ended for that person. If two individuals who love each other are permanently and completely separated in some way so that they are "lost" to each other, that would usually mean that the love they shared would also be lost, irredeemably changed into some other emotion.
However, none of these things will come to pass. Despite the onset of insanity, the person will still have a rational and "sane" existence. Even those who have drowned "shall rise again." Despite whatever circumstances occur to force lovers to be absent from one another, their love will continue.
The poem in general, as represented by these lines, uses strong rhythms and vivid but simple language to convey its message; the life force in nature will continue in spite of apparently terrible situations or events. Death is not the final event.