The sentence was rewritten.
Indeed, the ambiguous pronoun reference was removed altogether and the adjective "broken" was moved before the noun. This way,
- the information that the clock was broken can be conveyed in merely one phrase (the noun phrase which serves as subject of the sentence: "The broken clock") and there is no need for a relative clause;
- there is no more ambiguity because it makes it clear that it was the clock which was broken, and not the shelf.