Perhaps you can use manual data capture to change the box you want to tick directly with AMC?

That's exactly what I am doing, by going to "manual capture" and un-tick crossed out boxes after an "automatic-capture-mark-associate" process.

It's just that it's too much a hassle to go through all pages. That's exhausting (for >50 students and >50 pages per student) and error-prone. I partly reduce the hassle by noting in the name field pages where "manual" un-tick is needed during grading process. However, if students change their mind when answering multiple choice questions, cross out one and tick another, I won't be able to detect unless I still go through all pages.

Just while typing these message, I realized that I could query on the score.sqlite file to pull a list of questions scored "0" due to "more than one boxes are ticked"
select * from scoring_score where score=0 and why='E' (Is this sufficient?)
Then I should be able to generate a text file with student/page for further manual un-tick.

Then again, if at "manual capture" interface, I could load this text file to filter out unnecessary pages in the right panel, it'll make navigating through pages much easier.

Hope that I've clarified my points.

I realized that I could query on the score.sqlite file to pull a list of questions scored "0" due to "more than one boxes are ticked"
select * from scoring_score where score=0 and why='E' (Is this sufficient?)

This is sufficient (why='E' alone should also be sufficient). Those questions are also colored in red in the ODS export.