A general rule is that divorce = court = paperwork. If it's uncontested, there may be a do-it-yourself kit at the courthouse or online that you two can complete and file to get a final order of divorce. Call a family law attorney in your neighborhood and ask them what the procedures are for doing this yourself.
I'm a Florida litigator, not a CA attorney; so I'm just sharing my thoughts and not giving you specific legal advice. Good luck.
It's not clear from your question if you already have a Judgment of Legal Separation, or if you're simply separated. If you have a Judgment of Legal Separation (including division of any property and debts, child custody and support orders if you have children, etc.), then that case (call it "case file #1”) is essentially OVER, and can't be "converted" to a divorce.
You can, however, start a new case file for a dissolution of marriage. You'd pay the new filing fees, and the ONLY thing that will need to be done in that NEW case is dissolving the marriage; all the other stuff was done in case #1. You'll have to re-do SOME, but not all the paperwork, since your Petition for Dissolution should indicate that there are no financial issues to address because they've ALREADY been addressed in case #1.
I agree with Mr. Gould-Saltman. I would like to add what you can do if you DID NOT obtain a Judgment of Legal Separation, if you merely filed for either a legal separation or for a divorce but did not obtain a Judgment.
Although you could try to amend the Petition, you may not be able to, because six years have passed. You have exceeded the amount of time (5 years) that the court in California can leave a file open without action. You will probably have to file a new action for Divorce.
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