Hey! I wish I knew the correct procedure to do that as well. What I do is hit UNDO in the edit section, it's the only method I know works.
I'm sure some tech-head in here will supply an answer, then we'll both be the wiser.
Other forum members do lots more pixel work than I. You might want to look at the "Show us your work" section of the forum for samples of what can be done.
Note, neither Photo or Designer are focused on being dedicated "paint" programs like Krita. But there are some good tools.
I mostly do vector work, and am currently working on a 5K x 3K desktop image. I just opened it up, and added some 1 pixel wide line work to one of the vectors. I had to be zoomed in 81000% in order to make a 16 x 16 px drawing, each pixel a different color. Not even visible at 100% zoom, and only a dot at 150%. So I guess Designer nicely handles high resolution, and pixel level precision.