I have reversed the scroll direction in settings for xfce. The direction has reversed in gtk applications but it remains the default direction in qt applications.
The synaptics.conf file has this section in it:
# DO NOT EDIT THIS FILE, your distribution will likely overwrite # it when updating. Copy (and rename) this file into # /etc/X11/xorg.conf.d first.
For now, I have copied the xorg.conf.d folder from /usr/share/X11 to /etc/X11 and made the changes in the copied file. I have reversed the scrolling direction globally. Will see if any update breaks this.