Some eggs were still good, but the rest were all rotten.

Literal

Rotten-not eggs [also-も] some existed [but-が], remaining eggs [topic-は] all rotten-were.

腐っていない卵 (eggs that hadn't spoiled) vs. 腐っていた (were rotten) — the ~ている form marks the state in both cases. みな (all) is a literary variant of みんな.