@gromittoo ,
I have never seen that happen.
The only way I know of for the two Views to appear to have different font sizes is if there is a zoom difference. I know you said you returned to default zoom, but the two Views don’t sync zoom in modern Notepad++, so you have to return to default zoom for each View separately. (Click one view, reset its zoom; click other view, reset its zoom)
If your views are top/bottom, rather than left/right, they aren’t guaranteed to have the same number of rows, so right click on the divider between, and Rotate Left to get back to side-by-side views, which always have the same vertical space.
Alternatively, if the font sizes are actually visibly the same, by a given line takes up more vertical space because of line wrap, you can drag the separation bar left/right to balance the width, or turn off line wrapping.
I want to compare two files, side by side. My searches led me to use the View -> Move/Clone Current Document -> Clone to other view…
That advice showed two copies of the same file, and doesn’t compare two separate files. You can move (not clone) the second file into the other view, if you really want two different files side-by-side.
And if you’re really comparing two files, the ComparePlus plugin is your friend. (It can be installed using Plugins > Plugins Admin)