I want to convey that I encourage them to do further research and it
is okay to say something I disagree with as long as they support it
with proofs and evidence.
Then that is what you should say! Precisely that.
I appreciate your desire to get things right but always relying on others may be counterproductive. I encourage you to do further research. ...
I think the key here is your insistence on “trying to be polite and nice” and telling the student “politely”. I can’t say for sure, but I’m guessing your desire to be polite is getting in the way of clear communication. I’ve seen this happen with people who are so afraid of upsetting others that a lot of the time when they want to communicate something it ...
I usually set weekly or so meeting to discuss progress of my students. They are free to contact me in between if something important/urgent comes up.
I'd handle a situation like the above with a short answer, if needed, or just "take another look, we'll talk about it next time".
I'll assume you already have language that indicates your support. Don't give up on that.
But, ask him for two things. First, that he only asks for feedback once a week (or whatever you are comfortable with) and add a report on changes and why they were made.
Second, ask him to specify in the report things he is unsure about and to detail why he is unsure.