In principle you don't have to flip any image (and even less if you stack in RAW).
Nebulb always performs stacking with all images oriented in the same way. This is something that Nebulb manages internally based on the information of the images and their metadata (where the camera orientation information is).
Thus, the only thing you may have to do (when importing images into Nebulb) is to select the orientation of the base image (if it does not have the orientation you want).
In that case, before stacking, you simply have to rotate the base image to the orientation you want (with the rotate buttons on the top toolbar) and Nebulb applies that same orientation to all the images in the stack (without having to do anything else).
For example, this is the orientation that Nebulb shows me when loading a stack of images captured with a star tracker for more than 6 hours (time during which the camera has completely changed its orientation):
But since I wanted Orion to be vertical in this case, I simply applied a flip to the image (before stacking) and Nebulb already took this orientation into account for the rest of the images in the stack (regardless of the fact that there could be images with different orientations):
Thanks to which the final image was in the same orientation: