No, I can't say I've ever experienced the filters option disappearing. As I mentioned, the only time that option didn't work was when I first used the Photos app after the PC re-set. I can't remember just what I clicked on that activated the prompt for me to install the Photos Media Engine add-on, only that without that add-on the auto enhancer, and possibly the filters, didn't work.
If you look in your MS Store installed apps, and Photos Media Engine add-on is there then, as far as I'm aware, you should be fine ...... and if it's working ok now then maybe it was just a glitch.
I've just opened the app and auto enhanced a few photos and everything works fine.
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