I had highly modified audio and video encoder files. After updating the program, both files were removed and replaced with the program’s default files.
If Topaz adds new encoders to the program or makes changes to existing encoders (neither of which occurred in this case), just write them into the existing file.
This is a though or impossible request. Topaz needs to update the encoders file because they keep adding codecs and improvements to it. There is no fool-proof programmatic way for them to merge your changes with theirs. That usually needs human intervention.
Your best option is to save a backup every time you make changes to the encoders file. Every update that removes your changes, you’ll need to manually merge that backup into the updated file.