So, what was lost when Yuri "failed to negotiate her contract": two high-quality character models, worth thousands of dollars each. Associated artwork - backgrounds, intro animation screen, background music, end credit animations, and so forth. The cost of reworking the anniversary merch art and scrapping Yuri's anniversary merch designs. I might even be missing a few things from that. There's too many variables to make a good guess, but I'd be surprised if that wasn't at least $5K in lost materials. I don't think Sakana would have started reworks on her new character model though - her character model was fairly new and I think he would have at least waited for the renewed contract.
From what I've seen, Yuri was happy with her new model and had a lot of input into the new design. And whether it suited Yuri or not, it was a pretty good-quality model. Sakana didn't skimp on money when he was paying for it to be made.