The writers were commenting on productions, not canon when they said it's "still there".
1. Those writers are now the guys who decide
what is and is not canonical.
2. If they say that a line onscreen meant that the prime timeline still exists, then that's what that line means. Period.
3. They have said that a canonical line about alternate timelines means that the original timeline still exists.
4. Ergo, canonically, the original timeline still exists.