En doesn't only refer to indirect objects of the verb (and indefinite direct objects), but also to noun complements of the direct object of the verb.
For example, "J'ai lavé la moitié la plus sale de ma lessive" (I washed the dirtiest half of my laundry) has "la moitié la plus sale de ma lessive" as its direct object, which itself is composed of main noun phrase (la moitié la plus sale) and a complement prepositional phrase (de ma lessive). You can extract this complement phrase from the direct object phrase and turn it into a pronoun attached to the verb:
J'ai lavé la moitié la plus sale de ma lessive
J'en ai lavé la moitié la plus sale (I washed the dirtiest half of it or more idiomatically, I washed its dirtiest half)
It's likely that it is what's happening in the question's sentence, although it's not obvious without context what this noun complement would be. But let's invent an example to clarify the transformation at work here:
J'ai mangé les pommes de ton verger
J'en ai mangé les pommes
And it might become obvious that the difference between "j'en ai mangé les pommes" and "j'ai mangé les pommes" is identical to that between "I ate the apples" and "I ate its apples" in English.
The past tense has no influence of this, the same distinction would be obtained the same way with another tense, simple or compound:
J'en mangerai les pommes (I'll eat its apples)
Je mangerai les pommes (I'll eat the apples)