I finally had to read a walkthrough to find out how to make that door disappear. I found out that I had done the same thing with the slate a number of times, but I had linked out with the pedestal on top of the lab, instead of climbing down to the one inside. Why did this make any difference?

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It shouldn't matter whether you link to the bubble using the pedestal on the top or the pedestal inside the lab. The important thing is that you use a specific symbol on the slate to delay the bahro, and that you arrive at the door in time.