When I say original vs. altered timeline, I'm referring specifically to HRG's wild card actions. The rest was more or less predestined, or happened very similarly before and after HRG's actions. But shooting Erica was a clear alteration that hadn't already happened before HRG went back, and that led directly to Quentin's opportunity to get on the inside with Erica.
And again, we're dealing with multiple layers of time travel. Hiro and HRG went back from 2015 to 2014, and then the same Hiro took Angela and the kids back to 1999. He took them back to 1999 before HRG stepped on Erica's butterfly, so their roles from 1999 to 2014 proceeded as they always had / were predestined to. But HRG's actions in 2014 after they were gone potentially changed things between June 13, 2014, and the present.
And again, we're dealing with multiple layers of time travel. Hiro and HRG went back from 2015 to 2014, and then the same Hiro took Angela and the kids back to 1999. He took them back to 1999 before HRG stepped on Erica's butterfly, so their roles from 1999 to 2014 proceeded as they always had / were predestined to. But HRG's actions in 2014 after they were gone potentially changed things between June 13, 2014, and the present.