I think this supposition is very probably right. When you entered the Dragon Cave for the first time, did you clear the place out completely? If you didn't (and it's pretty difficult for a comparatively inexperienced party to get to the far reaches of the cave), then it's entirely possible that some artifacts were dropped in the remotest cavern and were lost when the cave respawned.
This is always a danger in the way I play the game, because I find the young dragon to be such a useful NPC that I tend to enter the cave very early. In the games I've played, some artifacts just don't show up no matter what you do. I played MM8 through 5 times before one of my parties finally found Elsenrail.
I've attached a link to a list of the sites in the game where artifacts may be found.