GTK 3 has support for dark themes with the boolean gtk-application-prefer-dark-theme setting. This means that, if a theme has a darker version available, it will use that version of the theme. Currently, because LXAppearance overwrites the settings.ini file for GTK 3, using LXAppearance to change the theme will reset this setting.
Even if LXAppearance doesn't actually have a way of configuring this setting, it would be nice if it detected it in the existing GTK 3 file and rewrote it alongside the existing configuration.
I believe this issue is completely fixed in the most recent release of LXAppearance (0.5.6). Try it, please, when it's possible for you and leave a comment if issue wasn't solved to reopen the report. Thank you very much.