I'm only guessing, but it sounds to me like you might have used the "Drop and Use" option with the first pyramid, which means that pyramid would still be down the hole. Perhaps you could try try using that option again with the second pyramid, to get down the hole to the first, drag it into your open inventory, then Use it (without dropping) to get to the second pyramid, so that you can drag it into your inventory.
At least it's worth a try.
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