The use of ethyl acetate as an extraction solvent as opposed to diethyl ether will not have an effect on the chromatography. I assume from your question that your sample remains disolved in the extraction solvent for injection (I assume GC here?). A change in solvent used in injection can affect the retention times of compounds close to the solvent peak. If your compunds eleute away from the solvent peak, you should not see any significant change. Having said that, if you extract significant quantities of other compunds, overloading of the column, would have effects in the retention of compunds eluting close to these overloading compunds.
I would note that handling organic acids in ethyl acetate can result in trans esterification. Be on the lookout for ethyl esters of your organic acids.
And for LC, it is likely you separate that analytes from the organic solvent - in which case the solvent would have no direct effect.