That's what I was thinking. When you think about it, the elements don't seem to be a conscious or even omnipotent force that actually maintains balance. If Harmony got up from its lazy bum once in a while, maybe there wouldn't be so much evil in the land running amok every time someone thinks life is unfair.
As for how it could effect the space time continuum, think about how it operates. Harmony needs 6 vessels to operate, which outputs a magic apparently stronger
than every other magic source that exists
When that magic is released, it seems to 'reset' an individual back to a certain state before they became corrupted. Think about it. The Nightmare was drained of her magic and 'restored' back to a supposedly younger version of Luna, unless she was the same age. Discord was returned to stone, a state that would be considered innate or 'without chaos'. Assuming that he has always existed and is therefore completely immortal under all circumstances, there could be no 'state' to return to. Perhaps he was just either drained of magic or returned to a state opposite that of what he was before Harmony came into play. And then you have Tirek, who was returned to the state before he escaped, exactly
But, I could be wrong and Harmony could simply be a force that drains magic from an individual.
But how could that affect the Space Time Continuum? I think by A) simply having a power more godly than time itself is bound to cause issues, B) altering time to destroy targets, C) causing instability in time by causing events in history to change from what they should have been, or D) another reason yet to be explained by the creator of this story.
I know I should not come to a conclusion like this, but we'll see...in time.