I just used o365cli to upgrade my project version from v1.1.0 to v.1.4.1.

spfx project upgrade --toVersion 1.4.1 --output md > report.md

The report appointed some json files to update.
However some of those were already created and had content within,so I wasn't sure if I was supposed to append the config, or if I was supposed to replace it entirely.

In my case, I just appended the config keeping what it was already there and that seemed to work for me.
Might be the case for other people's projects.