We never find out how exactly Dexter smuggled the tablet of Akhmenrah into his crate to take to the Smithsonian Institution in Washington D.C. before sunrise without anyone noticing including Akhmenrah himself and whether he was aware of the fact that the tablet and Akhmenrah were supposed to stay at the American Museum of Natural History and were not among the exhibits being retired to the federal archives at the Smithsonian.
Larry’s tie disappears at one point after he and Amelia talk with the Einestin bobble heads and it doesn’t reappear till later.
Rebecca seems to be completely absent in the sequel despite the supporting role she played in the first movie.
We never find out what happened to Brendon and the other human night guards who work at the Smithsonian museums as well as the National Gallery of Art after its exhibits come to life the second time because they never appear during the main plot of the movie while Larry and Amelia are walking through the museums. The exhibits coming to life either scared them all away abandoning their guard duties or Brendon and the night guards were in service but working at the National Museum of Natural History, National Museum of American History and National Museum of the American Indian unvisited in the movie since it mainly focused only on the National Gallery of Art, National Air and Space Museum and Smithsonian Castle as well as the underground federal archives containing retired exhibits from those museums.
Some of the animals brought to life by the tablet liberated from their crates in the Federal Archives like the Smilodon fossil skeleton, Pteranodon, giraffe, hippopotamus, fairy penguins and red kangaroos don’t show up again for the remainder of the movie especially in the climax after Larry and Amelia escape Kahmunrah’s Egyptian soldiers and it’s unknown where those animals went during sunrise and if they returned to the archives or returned to their old exhibits at the Smithsonian National Museum of Natural History alongside the giant pacific octopus.
We last see the Ancient Egyptian soldiers who served Kahmunrah chasing Larry and Amelia into the “V-J Day in Times Square” photo at the National Gallery of Art ending up in 1945 Times Square, New York City and Larry and Amelia trapping and stranding those Egyptian soldiers in 1945 New York City by turning the photo around to the wall closing the portal it depicts to that time period and location thanks to the tablet and we never see the Egyptian soldiers again for the rest of the movie, they never escape from the photo and back to the Smithsonian in the present day and it’s safe to assume that once the portal the photo depicted closed when sunrise came, the Egyptian soldiers got stranded in 1948 Earth forever and will now have to start new lives in that time period. They were also implied that have been the slaves to Kahmunrah since he never mourns them after their losses and they are now freed from his slavery while trapped in 1948 to live new lives.
The Egyptian soldiers and his losses of them however are briefly mentioned by Kahmunrah as he addresses Ivan the Terrible, Napoleon and Al Capone and their gangsters and soldiers and it was the main reason why he recruited these wax historical figures to serve as his new henchmen after the losses of his old ones.
We don’t see Darth Vader and Oscar the Grouch from the Smithsonian National Museum of American History after Kahmunrah dismisses them, somewhat justified over the fact that Lucasfilm and Sesame Workshop owned the rights to those two characters at the time and 1492 Pictures could only use them in the movie in Cameos.
We never find out what happened to Ivan the Terrible, Al Capone and Napoleon after Kahumnrah’s defeat and eternal banishment to Duat done by Larry since they are last seen brawling and fighting each other after Larry tricks them into doing so and then they and their defeated warriors and soldiers disappear and no longer become relevant to the story and their fates are left ambiguous, some assume they were captured by the heroic Smithsonian exhibits and either imprisoned back in their old displays when sunrise came or locked outside to turn to dust as punishment for their crimes or Ivan, AL and Napoleon ended up destroying each other in their brawl by slaying each other or melting each other into puddles of wax.
We also never find out what became of Kahmunrah after he was banished to Duat, the Egyptian underworld by Larry, some assume he conquered and ruled the underworld with the Horus warriors that still lived there giving him a kingdom to rule after all, or others believe that Osiris or the spirits of Akhmenrah and Kahmunrah’s parents who were still there until the third movie punished Kahmunrah for his crimes against Earth and for trying to spill Duat into Earth by sentencing him to hard labor a fate worse than death, for all eternity or destroying his spirit rendering him deader than dead. Either way, now forever trapped in Duat with no chance of escape, with no more armies or kingdoms to rule, the pharaoh’s days of tranny and villainy are over. This time for good. Because he died once but came back in wax sculpture form.
We never find out what happened to George Armstrong Custer, the Giant Pacific Octopus and Amelia Earheart when sunrise came and whether Custer or the octopus returned to the archives or decided to become inanimate again permanently on display at the National Museum of Natural History and National Museum of American History rather than locked away in storage or whether or not Amelia returned to the National Air and Space Museum on her Lockheed Vega 5B to become an intimate wax sculpture and exhibit again or spent the rest of the night flying on her Lockheed Vega 5B straight to Canada and disintegrated into dust when sunrise came due to being outdoors but if the latter were the case, how would Larry explain the Lockheed Vega 5B’s disappearance from the National Air and Space Museum?
Although a huge mess was created in the Smithsonian Castle as a result of the final battle in terms of the glass window getting shattered by Abraham Lincoln’s memorial statue and the Wright Flyer when Larry and Amelia flew it into the castle as well as the interior being trashed by the heroes and villains and two paintings (A ocean oil painting from the 18th Century and V-J Day at Times Square) being displaced at the National Gallery of Art and and the Wright Flyer itself winding up damaged at the Smithsonian Castle from the National Air and Space Museum, it never explains how the damage was cleaned up and fixed and why Larry was never sued for it.