Couldn't sleep, but I feel better now.
I've thought some more about the paradox idea and the more I think about it, the more I think it would be impossible to include in a coherent storyline: In order for duplicates to exist when Sam and Max discover the tomb, they would have had to timetravel before, otherwise the causality doesn't work unless we have a timetravel and a cloning device, which would be a bit much. We need another explanation and as much as it pains me, that means that the skeletons can't be Sam and Max.
The nearest thing I can think of right now would be:
After Sam and Max discover the tomb, they link it to ancient Egypt and head for the museum where an evil archeologist of some sort is experimenting to use the mystical abilities of certain artifacts from ancient Egypt to open wormholes to different times and places. The "artifacts" are actually inhabitants of Gordon's planet who, without being stripped of their body like Skunkape did, are able to assume the form of existing objects. They had studied ancient Egypt and laid dormant when it collapsed, until they were dug out by archeologists. The villain wants to use their powers to basically overcome a inferiority complex by fixing the timeline so that archeologists are seen as the cream of the crop (supported by an invisible puppet master with an agenda of his own). Sam and Max have to stop him and in the course of this they create duplicated of themselves from banana jelly and styrofoam which are prompty sent back in time during the final battle with the evil archeologist.
I think we can build a story on that.
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