Learn French: Des poireaux ? J'en ai épluché trois.

This is the core exception you are learning! Normally, a past participle agrees with a preceding direct object. However, when that direct object is the pronoun en, the past participle remains invariable. That is why we write épluché instead of épluchés.

Could I say Je les ai épluchés instead?

Yes, but it changes both the meaning and the grammar. Je les ai épluchés means 'I peeled them' (referring to all the specific leeks mentioned). Because you used les, the past participle agrees and takes an -s. The sentence above uses en because it specifies a smaller quantity out of a group ('three of them'), which triggers the no-agreement rule.

What exactly is en replacing here?

It replaces the partitive construction de poireaux. Because the speaker is indicating a specific quantity (three), the underlying structure is 'I peeled three of leeks.' The pronoun en steps in to mean 'of them' and works together with the number trois.

Why is trois placed at the very end of the sentence?

When you use a specific quantity (like a number) or an adverb of quantity (like beaucoup) with the pronoun en, the quantity word must stay in its normal position after the verb. Even though the noun it refers to has moved before the verb in the form of en, the number stays put.