When Eobard killed Barry's mother, Well's or pretty much anyone else shouldn't the same black hole event occurred.
Unless there is a Tardis involved, time travel story arcs are always messy lol
It wasn't a paradox.
Changing history is fine so long as time can wrap around to allow the core events to happen. But Eobard cannot exist without Eddie, and Eddie killing himself stops Eobard from existing - which cracks time wide open. Because now Eobard can't come back in time, which means everything from that day onwards in Central City never happens. And time can't repair itself.