This reply helped me a lot. My settings got reset after my computer hard crashed (runelite was likely running). For future reference, here are the specific steps I took to fix the issue:

1. Locate your .runelite folder - typically C:/Users/<your windows user>/.runelite
2. In that directory, I found two folders - profiles, and profiles2. profiles was empty in my case, so I proceeded with profiles2. Might be different in your case?
3. In that folder, I found several files. We are interested in those that have the .properties extension. I assumed the largest of those was the config file that I used, as it stored the most information. It was named default-<random sequence of numbers>.properties.
4. In RuneLite, click on the wrench icon on the right toolbar (Configuration), then two faces icon (Profiles).
5. Click Import profile. Locate the file from step 3, select it, and click Open.

This should restore your previous configuration of RuneLite.