I like to think that if she was alive and in her husband's life she'd have reached out to John to try to mend bridges before his father died, or at least let him know of his father's failing health. But then, John might not have ended up in Antarctica or he might have made a different choice and not gone to Pegasus so...

My headcanon is that she's dead and her death fractured the family irreparably, but then again maybe she was a deadbeat mother who bailed the first chance she got.

It's good to have somethings not addressed in canon cause it gives us a lot of leeway to create something when we write fics.