This is where I'll post what I think should be canonized into the TFTM-ROTF-DOTM continuity to explain some stuff. Skids and Mudflap's disappearance: They fought alongside the N.E.S.T. team stationed in Diego Garcia. When Optimus messaged them about the discovery of the piece of the Ark, they were flown back to the main N.E.S.T. base in D.C. They stay with the team. When the team escorts Sentinel back to H.Q. they are there, waiting.When he arrived, he betrayed them. Skids died blocking a shot aimed at BB. Mudflap attacked Sentinel for killing his brother, but was soon killed.