Ahora ya sé que lo eres

Ahora ya sé que lo eres
 

An example from a textbook:

Dudaba que fueses bonita: ahora ya sé que lo eres.

Why lo, not la?

The direct translation is I doubted that you were pretty: now I see what you are.

Lo que / or less commonly que lo means that which. La would be completely wrong. You could leave out the lo, but that would change the meaning, and that would make it less ambiguous. (now I see that you are).

The object pronouns "la", "los" and "las" ALWAYS refer to something that is identified explicitly or implicitly by a noun with the same gender and number.

The object pronoun "lo" does double duty:

a. "Lo" can refer to anything that is identified explicitly or implicitly by a masculine singular noun. In this case, "lo" is a masculine singular pronoun.

b. "Lo" can refer to any concept, idea, or phrase that is not or that cannot easily be identified by a specific noun. In this case, "lo" is a neuter pronoun.

In your sentence "(que) fueses "bonita" is not a noun: it's a verb phrase that expresses a concept, and verb phrases do not have either gender or number. As there is no noun that exactly represents that concept expressed by "(que) fueses bonita", the only object pronoun that can refer to "(que) fueses bonita" is "lo" in its capacity as a neuter pronoun.

Thank you very much, wrholt! I've had a hard time trying to link a pronoun to bonita :)