You've probably gotten all your prefs back to the way you like them by now, but just in case...
There's no telling what happened to your prefs. Updates won't touch them. They only replace the code bits. Usually if your preferences are "reset" it's because the application was unable to load them, and so it simply creates a new set of preferences from the default values. When this happens, the TD app will first make a copy of the existing preferences file that it is unable to load, giving it a new name with a timestamp in it. Then it will create the new preferences file. This is really only good for troubleshooting, but sometimes I've been able to salvage them.
You'll find your preferences file in your "Documents" folder. Open up Windows File Explorer (press your E key while holding down the Windows key on your keyboard). In the location bar, type the word Documents and then press the Enter key. Next look for the folder named "The Tournament Director 2". Open it. Inside here you should find a file named "prefs.sav". If you see another file named something like "prefs.sav.20200929-090258", then you'll know this happened at some point. That's the file that the TD was unable to load. If you've not gotten your prefs back to the way you wanted, you can send that file to me and I can take a look.
Also, when the TD is unable to load your preferences, you should receive an error msg upon startup of the application saying "There was a problem loading your preferences." (along with an error message). If you've never run across that, then I suppose it is possible *something* other than the TD moved or deleted your preferences file.