Hello and welcome to our forums,

That mainly happens because the upgrade is a two step process:

- the uninstallation of the old product
- the installation of the new product

During the uninstall, the registry keys are being deleted and the new values are written during the install process.

To avoid this, we can preserve the value of the registry key(s) when the user proceeds with an upgrade. To do so, you can proceed as it follows:

- Go to "Registry" page.

- Right click on the key(s) you want to preserve during the upgrade process -- > "Properties" --> "Operations" tab --> check the "Preserve key content" option --> and set the condition as it follows:
OLDPRODUCTS is a property which stores a list with the Product Codes of the older versions of your installation package. This property is set only in a package which upgrades another package.

Attached you can find a screenshot for your reference.
Hope this helps.

All the best,
Catalin