Price modifiers get overwritten

I have a lot of price modifier presets. They live in the config file at /system/user/addons/cartthrob/config/config.php
I just updated CT from v8 to v9, and the config.php file got overwritten, thus deleting my price modifiers
Luckily i had a backup, so i was able to reinstate them. However, this is not ideal going forward with new versions an future updates.
Or am i doing it wrong?