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The Hunspell folder in App\DefaultData\Config\plugins\Config isn't being copied into Data\Config\plugins\config on an upgrade.
I've found on installer versions of NP++, sometimes the main config file wasn't preserved if just installed a new update over old one. Don't know if that's fixed.
I started making a BU of the (main) config.xml file, then copying in. That doesn't help you now, but unless they fixed the problem, it may help in future.
The only situation this would happen is if you let the app crash (pull drive unsafely or have Windows shutdown and kill it) and then upgrade before running it again.
Sometimes, the impossible can become possible, if you're awesome!
I can't speak to the portable NP++, but the installer version from publisher's site, had the problem of not using the previous config file when upgrading - at least some time in the past. Seem to remember forum questions about that.
I've experienced it in the past. Maybe they fixed it relatively recently.
With the installer version, only scenario you mentioned that applies is improper Windows shut down & that didn't happen. Some other (installer) apps did the same thing for a time - uTorrent, for one.
The portable NP++ version may not do this - dunno, haven't used it, yet.
I missed that you said the installer version. Sorry about that. You're correct that our version doesn't have this issue. I forgot to check and realized that crash-then-upgrade is already protected against in Notepad++ Portable.
This is fixed in the Notepad++ revision I just posted.