Silversmote Ghoul's first ability looks at how much life you've gained in the turn, even if it wasn't on the battlefield or in your graveyard when you gained life. It doesn't care if you also lost life, even if you lost more life than you gained.

If you haven't gained 3 life by the time your end step begins, Silversmote Ghoul's first ability won't trigger at all.

If Silversmote Ghoul isn't in your graveyard as your end step begins, its first ability won't trigger at all.