Well, I'm still debating whether it's meta fictional gymnastics or actually really happening, as far as the time jumps are concerned. I suppose fromMarvels perspective it is the metafictional explanation they want us to take as readers. But it is an interesting problem, considering that despite the mathematics not adding up, we have to consider that another explanation connects the Peter Parker of 1960's to the Peter Parker of 2015. I keep going back to a WhatIf? Scenario, where Marvel wants Peter to have stories told about him in the 1960's, the 1980's, the 2000's and the 2015's. Unable to solve the mathematical problem, Marvel just sweep around them and ignore the inconsistency and just switch off the previous decades mathematics, and open a new chapter with Peter in the new modern age. I don't think they had any alternative.
That's why something like these Beyonders coming in and wiping away the physical evidence that the super heroes operated in the 1960's, by destroying that Earth-616, is such a convenient tool. The super heroes, when they return after Battleworld plays out, come onto an Earth where 1960 doesn't matter. The MU will start in 2015 or 2016, and that will be year 1. All flashbacks will be re gigged to just give the essentials about origin, and can be updated there and then if Marvel go that way, because the Earth that once held history of humanity is now gone, and all that remains is memory and experience.