Is there any way to have it so Jar Jar knew that Padme was Queen Amidala the entire time? Looking at Eddie’s tool, I see there’s the line “…but only if Queenie thinks it all right to tell you.” Maybe incorporating that line with Jar Jar & Padme’s first meeting creates a double meaning that’s more apparent on a second viewing, and cutting out Jar Jar’s shocked revelation when Padme reveals herself would seal it?
I cut out Jar Jar and Padme’s first scene together from my edit, which is a big step in the direction you want to go. Remove that scene, then cut out Jar Jar’s reaction to Padme being the queen. I think that’ll eliminate the question from the viewer’s mind.