The giant rift that opened above the city was a result of the massive paradox that occurred as a result of Eddie killing himself. Closing it effectively prevented the paradox from wiping out their timeline but caused the breaches into Earth 2. So it's basically been explained already and is in fact the cause of the season 2 problem.
Honestly, though, it's not a big deal. Technically the same argument could be applied to season 1. Eobard's actions in the past should realistically have resulted in such a drastic change to the future that he would have immediately been wiped out of existence. The dozens of other major events he changed probably would have resulted in the same thing. I doubt the show will get cancelled as a result of this. Frankly it would be more confusing if they tried to explain why things stayed the same rather than just glossing over it.
It's why I don't really have high hopes for the Legends spin-off. Season 1 had a lot of problems and plot-holes, Barry generally acting like an idiot, and then all the time-travel focused episodes were nonsensical as not a single one dealt with the issues of time travel consistent with the others. The final episode isn't even internally logically consistent and relied on very intelligent people not asking basic questions, taking Wells at his word. I can give Eddie a pass as he was a cop, but when you have five people in a room with advanced science degrees (Barry, Cisco, Caitlyn, Prof. Stein, Ronnie Raymond) and they all act like idiots... It was like fans saw Jay's helmet at the end and they simply forgot how badly written the rest of the episode really was.
I feel sorry for Jesse Martin. I wonder if he steadily thinks, "at one time I played a really well written police detective..."