you remember how we were all going crazy about how could it be that whatever happened, happened was true yet there was this alternate timeline etc, etc

Well now that we know this wasn't an alternate universe where the bomb went off, what if the bomb DIDN'T go off but instead the pocket of "negatively charged exotic matter" that Dr Chang was worried about hitting actually just pushed them back through time to the "present"?

In which case that would mean the bomb was still in the shaft - after the Losties jumped through time, chang and his men called it "the incident", built the swan over it and encased the bomb in concrete.

Just like at Chernobyl, eh Sayid? ;)