Um, that is what Chapter 11 is for. It plays an important part in free markets, which (in part) is in to maximize value for creditors over a straight liquidation (Chapter 7).
Chapter 11 isn't a freebie for Republic Airways or anyone else to simply tear up contracts it doesn't like. With few exceptions, reorganization under Chapter 11 must be approved by the creditors.
Also, Chapter 11 includes special provisions for airlines (Section 1110) which requires Republic to continue all obligations regarding current leases through the bankruptcy process.
However, any reorganization plan proposed in court will likely reflect Republic's "single fleet type" strategy with a ton of concessions to Embraer. To put it another way, there would be absolutely no room for the CSeries under a reorganized Republic.
That is unless Republic's parent company (Republic Holdings) creates a new airline with a new business model to fly the CSeries. While anything is possible, chances of that happening now would be near zero.