Learn Farsi: ما ضایعات فلز را در کوره ذوب می‌کنیم.

No, in this sentence در is just the standard preposition meaning in or inside (در کوره means in the furnace). It is a good reminder that while در is used mathematically for proportions (like یک در ده), its most common everyday role is still just locating things in space.

What is the grammatical structure of the word ضایعات for scrap?

ضایعات is a plural noun formed with the Arabic plural suffix ـات (-ât). It refers broadly to wastes, losses, or casualties, and in an industrial context like this, it means scrap. The singular form is ضایعه, which usually means a lesion, loss, or tragedy.

Why does the object marker را come after فلز instead of right after ضایعات?

The marker را always follows the entire direct object phrase. Here, the direct object is the noun phrase the metal scrap, linked by an invisible ezafe as ضایعاتِ فلز. Because فلز is the last word in that specific noun phrase, را attaches directly after it.

Does the verb ذوب کردن work for both melting metal and ice melting on its own?

ذوب کردن is strictly transitive, meaning to melt something else, which is why it takes the object marker را here. If you want to say something melts on its own (intransitive), you must use ذوب شدن (to become melted). For ice specifically, native speakers usually just say (to become water).