Using ground based magnetometer data and an in-house developed quasi two dimensional (QTD) theoretical ionospheric model, we investigate differential response of the E region ionospheric current system to the solar flare events which occurred on 20 February 2002, and 24 September 2011. An abrupt increase in $\Delta$H (positive crochet/Solar Flare Effect (SFE)) was observed at Thirunelveli during 24 September 2011 event, while a decrease in $\Delta$H (reduced crochet/SFE) was observed during the other event. The reduction in $\Delta$H was observed on 20 February when there were no signatures of counter electrojet (CEJ). As per QTD model simulations, the ratio of integrated Hall to Pedersen conductivity decreased more on 20 February at EEJ heights. As the conductivity ratio is directly proportional to the vertical polarization field, a decrease in conductivity leads to a reduced EEJ strength on 20 February 2002. In the presence of an additional SFE current system at the boundary between D and E region, during solar flare, the crochet is the resultant of EEJ and SFE. On 24 September, both the EEJ and SFE current systems were strong with the vortex center close to the equator and a positive crochet was observed. On 20 February, on the other hand, both EEJ and SFE were weak as the current vortex was away from the magnetic equator. Hence we surmise that SFE not only depends on the strength of the solar flare or the background electrojet condition but also the position of vortex of current systems.