No. I was at Sunlight (\o/) covenant rank 3 before I temporarily switched over to Pilgrims of Dark. Got rank 3 there too, and then went back to the Sun. You can check your covenant rank at any time by talking to the cat in Majula.
Haven't verified it but A german Spy has stated in one of his vids that you keep all your ranks except for the two that are at war with one another. The Blue (Protector) versus Red (Invaders) one.
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