Hi @awineidea
I just did few tests to be extra sure, and to sum up your issue, it looks like that it is caused by outdated Advanced Filters add-on. You have version 2.0.4 which is a bit old (this version was releases 9 months ago), and more importantly incompatible with ShopMagic 3.0. This incompatibility may cause the filter to not be usable (which translates to “disappear”), but can be easily fixed with updating the add-on to the newest version (2.1.0).
Update should be available through WordPress > Plugins if your API keys are still valid. Alternatively, you can download the files from your account, which were created when you bought the plugin.
None shady practice occurred in this case. We did not cut any filter from free version. Newest ShopMagic core update simply requires updating all add-ons which you use because of numerous changes in the code.
As I wrote earlier, as this issue is strictly connected with paid plugin version (you are using paid add-on) contact us directly through our website.
Look forward to hearing from you!