In the handbook, it describes Bernard as a brainiac, and smarty pants (for some reason I only underlined brainiac) It's not that hard to believe that Bernard used his intellect to get the parts he wanted from Felix.

now you may be wondering, "Penguin man, why would Bernard want Felix's parts? isn't Felix just some gambler animatronic?" while he may be a gambler, in his heyday, he was jacked and had deadly pieces on him, such as a horn on his nose, and sharp claws. Bernard being the scrawny bunny he is, concocted some sort of plan to make Felix's strength and other body parts his.

in the image below, you can see that Felix has a horn on his nose, and sharp claws. the horn being a staple feature of Bernard, and the claws having the same lines (presumably where the metal opens to allow for finger flexibility, as seen with the Felix's hand gesture) and if i may take this further, Bernard has the same jaw shape and sharp teeth as Felix in this poster. It's safe to assume that if Bernard took his fingers body and nose, he probably took his jaw too. that would also explain why Felix is lacking a jaw in the game. also, futher evidence for Bernard taking the nose is that when you look at Felix in game, you see a nub where the horn was supposed to be

this arm looks almost identical to Bernard's arm, with the only difference being stitching. (yes, I checked Bernard's arm to see if the stitching matched, and the stitches were in different locations) and you might be saying, "but Penguin man, you tin foil hat wearing nutjob, Felix looks nothing like that in the previous image". well dear readers, the posters are not very accurate when portraying the animatronics. it's safe to assume that these posters were made before the New Jersey animatronics shipped to Pennsylvania. New Jersey Bernard most likely looked the most similar to his poster counterpart, similar to Clara. I think that Felix once looked like Bernard, and Bernard used to be a scrawny little smart bunny.

further evidence to support Felix's muscular physic is this child's drawing.

After Bernard stripped Felix for his parts, it scared Felix both physically and mentally. the physical part is obvious, but the mental part is a bit more nuanced, with Felix showing slight fear when he sees Bernard

Felix below staring at the ceiling without a care in the world

Felix sees Bernard and looks at him in pants pissing fear

I have 2 theories for how Bernard got Felix's parts.

1st theory is that Bernard got Felix to bet his body and Felix lost. We all know that Felix likes to gamble. But what if he decided to bet with his body? Bernard most likely rigged what Felix was betting on by doing smart stuff, and Felix had to give his body away. Not expecting this outcome, Felix was left traumatized by being pulled apart, and having his body being grafted onto Bernard.

2nd theory is that Bernard used his intelligence to create some kind of device, weapon, or tool, to remove Felix's parts. this would instill fear into Felix, which is why he looks at Bernard fearfully in cam 3.

there is one thing I'm not sure of, but I intend to find out. that being why Bernard hates Felix. and some of you might be wondering "Penguin man, why does Bernard hate Felix?" and to that I say, I JUST TOLD YOU I DON'T KNOW. we see Bernard grab Felix and kill him if they both appear at the same doorway, and Ryon himself has confirmed in a stream that Bernard hates Felix. This is perhaps something that shall be answered in the final game. the only thing I really know is that it wasn't always this way, as we can see them on a TV together looking all happy. Who really knows though, I could be wrong about this. maybe Green Boy stole these parts. I don't have the full picture yet, but I'm working with the pieces of this puzzle that I have access to. and remember, this is just a theory............A GAME THEORY!!!!!!! Thanks for reading