If Helix Pinnacle leaves the battlefield before its triggered ability resolves, check the number of counters that were on it as it last existed on the battlefield.

Helix Pinnacle’s triggered ability has an “intervening ‘if’ clause.” That means (1) the ability won’t trigger at all unless Helix Pinnacle already has 100 or more tower counters on it as your upkeep begins, and (2) the ability will do nothing if Helix Pinnacle has lost enough counters such that it has fewer than 100 counters on it when the ability resolves.