Turning on HD switches the default core/emulators.

You have 2 options:

1. Turn on HD mode for all games. Go into each game that you don't want HD, and set it back to the default core/emulator.
2. Leave HD off, and select the emulator that supports HD per game.

See:
https://wiki.recalbox.com/en/basic-usage/features/hd-and-widescreen-modes