Demo step by step:
Step1: creat a job as maven2/3 project
Step2: make a copy of the job's config.xml as config-old.xml
Step3: update "Root POM" of the job from UI to "pom-new.xml"
Step4: update the job using "update-job" CLI Command with config-old.xml
Step5: Checking....
(1) from the backend, the config.xml is the same as config-old.xml!
(2) from the UI side, it's "pom-new.xml"!

Step6: reload configuration of Jenkins, back to normal!

So, we got it!
"update-job" CLI command has a bug when update "Root POM", just like change the config.xml directly.