Hey! Got a few ideas here:
1. Are your custom animation files built on the default ones? Unity keeps track of what files are what with metadata files, so even if you change the included waves, when you update, it'll think that the update's wave is the one you want. If this is the case, you can create a duplicate (ctrl+D) to copy the wave but get new metadata. As long as there isn't a name overlap, that should do it.
2. When importing, uncheck the "Resources" folder.
3. You can create a new directory elsewhere with the name "Resources/STMWaves" and place data in there. All that matters is that it needs to be a folder named "Resources" and then the correct subfolder name for the data type.
At the bottom of the text data inspector, there's a button to gather all data, so you may have to press that to manually gather data that hasn't been created through the inspector. It's also possible that the main settings file is being reset on import, and this button just needs to be pressed, too?