I see a vertical video in the project monitor and I went and selected a vertical preset in the project settings as well.
However, the render is the usual 16:9 and one part where I had used the 'zoom and pan' is just blank.

Any help will be much appreciated.
Thanks.

you have to place AS FIRST CLIP a "vertical" clip ... Kdenlive is suggesting to switch the project to a "vertical" one (ACCEPT THIS) ... after that... everything you do will be rendered on "portrait/vertical" format.

this is what i do everytime i need to create a "youtube shorts"