Does the clock for suing restart if I only discover a second, separate problem later?

Not in the sense of reviving an old, already-expired claim, but a genuinely new problem generally does start its own fresh clock. Each distinct claim or cause of action is typically assessed on its own discovery date, both under Ontario's general limitation law and under whatever survival period applies to the specific representation involved — discovering a second, unrelated problem later doesn't retroactively revive a claim about the first problem if that one is already out of time.

What it does mean is that the second problem gets evaluated independently, on its own facts: when it arose, when it was discovered or reasonably should have been, and which specific representation or covenant it ties back to in the purchase agreement. If the two problems are actually connected — the same underlying misrepresentation surfacing in two different ways, for instance — that connection can matter to how they're characterized, so it's worth having both assessed together rather than treating the second discovery in isolation from the first.