Sadly it will, your CRS will change, as correctly pointed out by
@comfortablynumb here, you need to have 3 years experience in one NOC only, if you wanted to add 3 years experience you should have chosen the other NOC as primary in which you have 4 years experience.
Now if (as I understand) you have claimed points for 3 years experience, it means in your pre-ITA file also, you must have mentioned wrong NOCs too, because the system couldn't have given you points for 3 years untill and unless they were in the same NOC, as in your primary NOC you have only 2.5 years of experience and system can never give you 3 year points for that, there is some other anomaly here.
Please tell us properly what you mentioned in your EE file, the information you got ITA on.
Because the way I am seeing things your CRS will change after you send this CSE and you will become ineligible as your points will be considered declared wrong by them. And even if you don't send a CSE they will check this through your duties that you mentioned wrong NOC, you are in trouble either way I guess.
Give us more information here, so that we may guide you better, i.e whether this is just post ITA mistake or pre-ITA?