Without any kind of pictures it's impossible to follow what you are talking about.
One common use of HDMA is to change the scrolling midframe for a vast panoply of effects. Is it what you are talking about ?
Seems each BG layer of the SNES has 2 scrolling registers for X and Y directions, and the registers themselves are 16-bit, you need to write twice to change all the scrolling bits (except if the BG map is only 32x32, where 8-bit is enough and high bits can be ignored).
In all cases, HDMA can affect scrolling of any layers just by changing which registers it will write to.