。
The food has gone completely cold.
Literal
Cooking [subject-が] has-gotten-cold-regrettably.
A triple stack — 冷える + てしまう + ている — combines the 'unfortunately completed' nuance of ~てしまう with the resulting-state ~ている. 冷える emphasizes becoming thoroughly chilled (versus 冷める, which is more about cooling from a warm state). The plain form gives this a more casual, complaint-like feel.