All collectables will reappear eventually, it just takes a long time.
In my previous game, I was able to collect all of the temple relics and all but one of the science relics. The rares for the science relics actually hadn't appeared for a long time in that game and by the time I had finished everything, there was one relic that had yet to appear. Going by the shadow, it looks like some kind of book.
In my current game, I managed to fill the relics up pretty quickly for both, but haven't yet found two of the science rares and one of the temple rares.
You can go long stretches without seeing rares, so if those are the ones you are looking for, you'll just have to be patient.