The backbending phenomenon in $^{48}$Cr has been investigated using the recently developed Projected Configuration Interaction (PCI) method, in which the deformed intrinsic states are directly associated with shell model (SM) wavefunctions. Two previous explanations, (i) $K=0$ band crossing, and (ii) $K=2$ band crossing have been reinvestigated using PCI, and it was found that both explanations can successfully reproduce the experimental backbending. The PCI wavefunctions in the pictures of $K=0$ band crossing and $K=2$ band crossing are highly overlapped. We conclude that there are no unique intrinsic states associated with the yrast states after backbending in $^{48}$Cr.