Guanidine hydrochloride is a strong chaotrope that can be used to solubilize misfolded/aggregated protein, as you found. The GdnHCl must then be removed in a controlled way under conditions that favor refolding of the protein into its native state. A variety of methods can be used for this purpose. There are also kits available to assist in finding conditions for refolding.

In many cases, high-level expression of recombinant proteins leads to the formation of protein aggregation commonly called as inclusion bodies. In order to obtain biologically active and soluble protein in high yield, this procedure is carried out in three phases: isolation and purification of inclusion bodies, solubilisation of aggregated proteins and refolding of the solubilised proteins.

The first step is isolation and purification of inclusion bodies. The following link about inclusion body purification may help you :

The purified inclusion bodies are resuspended and incubated in buffer containing a strong denaturant (usually 8M urea or 6M GdnHCl) and a reducing agent (usually 20 mM DTT or b-mercaptoethanol).

Refolding of the solubilised proteins is initiated by the removal of the denaturant. Different techniques have been designed to recover correctly folded proteins from inclusion bodies including dilution, dialysis and chromatography, etc.

For more info about protein refolding, you can refer to the following link:

http://www.biologicscorp.com/inclusion-bodies-purification-protocol/.

http://www.biologicscorp.com/protein-refolding/