Prevent Windows Update/Upgrade to reset registry value(s)

Question

Situation:

1. Windows 10 with specific application installed
2. Application has modified some registry keys at installation in "HKLM\Software\Microsoft\Windows NT\CurrentVersion\Print...
3. After installing the Windows 10 update/upgrade (Version 1511 10586.3) registry values are reset back again, resulting in the software that is not working on many PCs (because registry value have changed/reset)

Question(s):

1. Is there a way to prevent Windows from resetting some registry values that have been modified? (can they be marked somewhere?)