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I've have set the execute command to ctrl+F6, and the direct execute previous to F6. Sometimes notepad++ reverts these settings, sometimes not.
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Not just shortcut keys - all custom config. This seems to happen when Notepad++ is closed and restarted within a few seconds of each other. My best guess is that, because the application is still saving data to the configuration files when it is closing, the new "instance" cannot access the config files and overwrites them with the default whenever the new "instance" is closed. (Especially annoying on a thumb drive as the slower disk access causes this to occur more frequently.) Using Notepad++ 4.9.2