If you find you are continually losing activations on your program the problem could be due to running a registry cleaner application such as CCleaner. Most registry programs give the user an option to deselect the items to be removed.
Due to the many different registry cleaning programs, it's difficult to say whether yours will have an option to 'whitelist' registry keys. White listing means that the software will ignore the selected information.
It's best to contact the developer of your specific product to see if they can block certain registry keys from being installed.