Harker travelled back to the earliest time period from 2053. If the bomb didn't go off the chain of events that resulted in Elias being born is broken and results in Elias never existing. I'm fairly sure that is what was meant, but not 100%
Yeah, it's a little lame. It's all pretty coherent until they decide they need a happy ending and the cycle is anyway broken. Then people start disappearing when it's convenient (just after the hugging) and we have the typical time travel paradox (how was the chain broken if Elias never existed? why would there be imprints on people's minds anyway?). That wasn't an issue when the cycle still somehow happened anyway.
Why did Maplewood go to 2023 at the end?
Was she trying to become Harker/Mannix?
I'm pretty soon that final scene is just a teaser for another season. The very final shot also shows KYAL (Know You Are Loved) being projected on the building next to The Gherkin. I'm assuming the story will be that things anyway get messed up somehow in the future (maybe an attempt by the writers to resolve the paradox), and Maplewood again had to time travel to fix things.