Yes it’s scary at first deactivating plug in’s but they keep all their settings for when you reactivate them 🙂 The only one that doesn’t seem to is Marketplace as I lose all my menu’s if I deactivate that one.
I’m guessing that Marketplace update interfered with your Search and Filter plug in (if that’s the only one you updated recently). That’s why I hold my breath every time I update plug ins! Many people run a staging site for testing conflicts before going live. Something I need to do!