Technically, it sounds like you violated the code and therefore you could be prosecuted for the violation. I really don't know how Los Angeles approaches code enforcement, so you need to talk to the City and see if they will let you off the hook if you agree to bring the property back into compliance. If it was one of the cities I've represented, we would work with you to get the violation corrected and that would be sufficient, but that doesn't necessarily mean that your city will do that. Each city is different when it comes to how they approach code enforcement, but cooperating with them will be in your best interest in getting things resolved...
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It would depend on what the citation says, but from what you state in your question, bringing the building back within what was originally permitted should correct the citation. You may want to contact the contact person on the citation to see how to correct the illegal construction. If the building is tenant occupied as two residential units, there may be additional issues that could be raised as a result of the citation.
Talk with the City about your plans, but more than likely, if you return it to its legal status as a SFD, the City will more than likely allow it. It may require you to obtain a building permit and have the work inspected, especially if the previous changes involved any structural, electric or plumbing.