。
The medicine's effect had worn off.
Literal
Medicine [gen-の] effect [topic-は] had-disappeared.
消えていた is the past of ~ている, giving a past perfect sense — 'had (already) disappeared (by that point).' 効果 ('effect, efficacy') is a Sino-Japanese compound commonly paired with medicine, treatment, and measures. A concise way to convey that the effect is gone before the reference time.