I was experimenting with the filters to view the glyphs differently. At one point I deleted them all, assumed it was just for the font, but apparently it was app-wide and across reboots and now when I try to create new filters they don’t show up in the list. Deleting and reinstalling the app don’t work. Do I have to clear all the app-data at some location or something?
Do you have a backup like Time Machine? The filters will be stored there.
Otherwise, if you want to restore the default filters (as there were after the first launch), choose Script → Open Scripts Folder. A Finder window will open. Delete the file called CustomFilter.plist and relaunch Glyphs.
In case you have a backup, this CustomFilter.plist file is the one you should restore.