The file kptsmap is only needed when the keyword bzsym is specified in the JobList in inp.xml.
The file "kptsmap" specifies the symmetry operations needed to map the k-points in the file "kpts.xml" (reduced set of k-points when bzsym is specified) to the k-points in the file w90kpts (entire Brillouin zone).
First column: Index of a k-point from w90kpts. Second column: Index of a k-point from kpts. Third column: Index of symmetry operation that rotates the k-point in the second column into the k-point in the first column. The rotation of the k-point in the second column might differ from the k-point in the first column by a reciprocal lattice vector, which is specified in columns 4-6.
Instructions on how to use symmetries in calculations of MLWFs is given here: Use of symmetries in Wannier function calculations