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I've noticed that each time a fullscreen mode is disabled for a window, its size is reduced.
It appears that sizes of top and left borders are subtracted from width and height respectively.

Demo:

    SDL_Init(SDL_INIT_VIDEO);
    int w, h;
    SDL_Event e;
    SDL_Window *handle = SDL_CreateWindow("", SDL_WINDOWPOS_CENTERED, SDL_WINDOWPOS_CENTERED, 800, 600, 0);
    for (int i = 0; i < 3; i++)
    {
        SDL_SetWindowFullscreen(handle, SDL_WINDOW_FULLSCREEN);
        while (SDL_PollEvent(&e)) {}
        SDL_GetWindowSize(handle, &w, &h);
        printf("[%d;%d] - fullscreen\n", w, h);
        SDL_Delay(3000);
        SDL_SetWindowFullscreen(handle, 0);
        while (SDL_PollEvent(&e)) {}
        SDL_GetWindowSize(handle, &w, &h);
        printf("[%d;%d] - windowed\n", w, h);
        SDL_Delay(3000);
    }

What it outputs:

    [800;600] - fullscreen
    [794;575] - windowed
    [800;600] - fullscreen
    [788;550] - windowed
    [800;600] - fullscreen
    [782;525] - windowed