Hiya what a handsome rabbit! Rabbits thump when they are scared to signal danger to the rest of the warren. they also thump to show their displeasure. I posted a similar post a while back because my rabbit Boo would also thump when i put her in her cage. I think thumping was her way of saying " i dnt like this"

Like Tallullu mentioned, usually thumping is a way to show fear, anger/disapproval, and can also be a threat/warning.   Was she doing binkies and just sounding like she was thumping or was she really just sitting there in his room and thumping?

If she was, how old is your son?  Could he have toys, or some object that Cuddles was feeling fearful of?  I know my bunnies will freak if there is something new, like a bag or box in the living room.  They will go closer, then thump, and thump and thump, and when they see no reaction, they slowly approach.

 

My bun definitely thumps in his cage when I pay more attention to my two lionheads instead of him