No you could still move for a finding of factual innocence but these motions are really hard to win. They're usually reserved for cases of identity theft. You got Prop 36, apparently completed the program successfully, meaning as you say the conviction is deemed not to have occurred. I'd be content with that before running up lawyer's fees ina futile attempt to prove it never in fact happened.
I have had pretty good success with factual innocence petitions in a variety of cases, but in your case you have a very large problem with having waited four years. The factual innocence statute, California Penal Code Section 851.8 allows you two years from the date of the arrest to petition for a finding of factual innocence. You are far past that time limit. The statute does also give the Court power to excuse the time limitations, but you need "good cause" why you did not act sooner. If you had strong evidence that you actually were innocent, a judge might be inclined to find "good cause" for the delay.
The benefit of course to pursuing factual innocence relief is that they first seal the arrest record and then after three years, they actually destroy it. So must the court, Prosecutor, Attorney General and police agencies.
I can't imagine many situations where a finding of factual innocence would be made if you pled guilty to the offense or were convicted at trial. It is theoretically possible, I suppose, but the petition should be denied if there is reasonable cause that you committed the crime – regardless of whether there is proof beyond a reasonable doubt.