This is more of an issue when syncing to anything before acquiring Stone III.

Why not make it so that Stone III was a trait which increased Stone II damage after you obtain it.

This way, whether you're synced or not, your main Single Target DPS spell wouldn't need to change.

Current state:
Get synced, swap out Stone III for Stone II on hotbar.

Proposed state:
Synced or not, Stone II remains on hotbar.