In the context of the question, the 10-dimensional spacetime is R1,3×X where X is a Calabi-Yau 3-fold. Considering type IIB string theory on this geometry, without branes and with no fluxes turned on, gives rise to an effective theory on R1,3 with N=2 supersymmetry. If one wants to go from N=2 to N=1 supersymmetry on R1,3, one can try to add D-branes. If one wants to preserve Poincaré invariance of R1,3, the D-brane has to fill in entirely R1,3 (it is interesting to consider cases where one does not preserve Poincaré invariance of R1,3 but I don't think that it is the context of the question). So the only possibilities, given that Dp-branes in IIB string theory have p odd, are D3-branes wrapping 0-cycles in X, D5-branes wrapping 2-cycles in X and D7-branes wrapping 4-cycles in X. In particular, there is nothing to wrap around a non-trivial 3-cycle.
Starting with D5-branes wrapping some non-trivial 2-cycle S2 in X and realizing the geometric transition consisting in shrinking S2 and growing up some S3, one can ask what happens to the theory: the D5 branes disappear, so how is it possible to still have N=1 (and not N=2)? The answer is that now there is a non-zero flux through S3 (it is a field strength flux for the 2-form gauge field present in the Ramond-Ramond sector of IIB. Remark that the D5-branes are magnetic sources for this 2-form gauge field and the idea is that during the geometric transition, the D5-branes disappear but the corresponding magnetic field remains).