Joe Clay | May 29, 2017
So, as I said last time, saving presets can be a real pain in After Effects. But it doesn't have to be—I think. I could be totally wrong. And well, I kind of was. It turns out that if you do as I suggested before, you might lose things when you select the main groups in a layer's properties, like Effects or Transform. Sure, it'll save the name. But if you apply the preset to a layer that already has effects, they'll be overwritten—aka removed completely and replaced—with the ones the preset has saved. This even happens with transform properties. If you save the whole Transform group in your preset, and you apply the preset to a layer that has any of the properties set or keyed, they'll be replaced.
So, we're going back to the old tip of having to save the sub-level items, like position, rotation, or an effect specifically. If you rename your effects and you click on it to save, it'll keep the name.
But what about shapes? You can rename them and save them by clicking on the shape/group. So basically, instead of selecting the major group—like Contents—you select the immediate sub-objects of each of those main groups that you want to retain. And unless you want to get really specific with certain keys, I wouldn't bother attempting to select them directly unless they're Transform properties—and in that case select the property itself and not the keys.
Also FYI, the latest update of 2017 still wants to save presets to the 2015 location by default. So that's fun.