hello aspirant,

NO, it will not affect your JEE preparations if you do not have done your Chemistry preparations in class 9th and 10th well. JEE mains chemistry section questions are totally based on the class 11th and class 12th syllabus and the questions for Physics, chemistry and Mathematics are asked from class 11th and class 12th only. So, class 9th and class 10th subjects (Physics, Chemistry and Mathematics) do not have any significance in JEE mains examination.

But still, if you have the fundamentals clear, for the subjects in class 9th and 10th, then it wouldn't be much difficult for you to cope with the class 11th and class 12th syllabus.

Further, to know more about the JEE mains syllabus and Exam pattern, you can follow the below mentioned link to know more : https://engineering.careers360.com/articles/jee-main-syllabus

I hope that this will help.