Notepad++ Portable upgrades are resetting the PluginManager.ini & SpellChecker.ini files. Removing the empty App\Notepad++\plugins\Config folder before running the new version fixes this.
EDIT:
App\AppInfo\Launcher\Notepad++Portable.ini
[DirectoriesMove] -=%SystemDrive$\N++RECOV
Shouldn't that $ be a %?
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Both issues are fixed in 6.3 Rev 2.
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