“base” Notepad++ has no problem with File > Reload From Disk. The symptoms you have described are almost definitely related to the HEX-Edit plugin, not Notepad++ itself. You can try to put in an issue here, but there are a lot of open issues on that plugin, and I won’t guarantee that it will be fixed. (The release history over the last few years seems to focus mostly on “crashes”, not any new features or minor bug improvements.)