The w90chk2chk utility (to convert to a machine-independent format the checkpoint file) sits in the main trunk folder of the Wannier90 distribution.
To get it, just go in the main Wannier90 folder and execute
make w90chk2chk
which will produce the w90chk2chk.x file.

For any further information on this utility, please refer to relevant section of the 'Utilities' appendix of the User Guide.