I have "Remember Current Setting for Next Launch" disabled. Every time Notepad++ is updated this setting becomes enabled.
The alternative is to install from an archive. But then whenever the various configuration files change with successive Notepad++ upgrades, the configuration files change and are no longer in sync with Notepad++. You may mpse new functionality and even get unstable behaviours.
The clean way to proceed would be to install from archive, check the differences between old and new congig.model.xml as well as langs.model.xml - the other files rarely change - checking the differences between factory version isn't bad after all.
Of course, a better way would be or N++ to check and upgrade the config files when it installs over an existing fileset. Then, it would have to be smart enough to, when installling 6.4.5, detect that you currently have 6.2.1 with old files from 6.1.4. This could be a little too hard to implement.
Here's how I'd do it:
1/ Design a stand alone updater for configuration files. This .exe would check your file against the version of notepad++.exe it finds, upgrade files as necessary and then brand the files with a new <verion ....> tag. The program could also know how to upgrade from version a) to version b). The job of the .exe is just to read the files line by line and check whether option x is present, adding default values, and commenting out obsolete options it finds on the way. A plain text filter.
2/ Installer would run this if no version tag is found.
3/ Installer would upgrade your files to the version it is installing.