In january jee mains I have entered my category as general because at that time my obc certificate was not prepared but now my obc certificate is made so for april attempt I have entered my category as Obc. So I have a doubt that would my january jee mains score would be counted or not?
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Your both JEE Mains score is counted since it is your marks based on your merit which is very true . And correction is provided so that you can correct your details which you have mistakenly entered. So there is no problem in changing the character as far as what I know .
If you will use your score of JEE mains January session then you will be considered as general candidates since you applied in that attempt as general candidate.If you will use score of JEE mains april session and if you have applied as OBC category candidate then at time of counselling you will be considered as OBC candidate and you will have to show your valid obc certificate.
I Hope this helps.

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