I don't think they deliberately misdirected your ballot. There are so many ways for it to get messed up, it might even be the County Board of Elections in your local county. 
My suggestion is to consider voting in person this once - just to make sure your vote gets counted. You'll have more time to look into the mailed ballot option after the recall voting is done. And hopefully Newsom will still be in office when it's over.
If it turns out you do need to re-register to vote, do it early and online. Request the mailed ballot for next year. When you register keep in mind that you'll be asked to show ID after you register, and they probably want a CA drivers license or a US Passport. Your voter registration needs to match your physical photo ID card in every way - same name, address, everything. If you have either one of those you're good to go. If you don't have either, you can still register and vote but they'll make it more complicated for you.
Good luck my friend!
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