I suspect Bombardier already had them by the balls, after their disastrous legal bad-faith manoeuvres.
They are lucky that the renegotiation will get them all in time for Eglinton, rather than strung out more for Finch West and Sheppard East. Given that Metrolinx said they were doing this because Bombardier couldn't deliver Eglinton in time, it seems odd to me that they've negotiated for all the Bombardier units to go on Eglinton, rather than using them in the original design for Finch and Sheppard, etc.
Though presumably the Mount Dennis yard design makes a change difficult at this point. Which presumably means that Bombardier will get the Sheppard East, Eglinton East, and Eglinton West orders as well. While Alstom would presumably get Hamilton, Mississauga, and the Finch West extensions to Pearson and Yonge.