Unfortunately the HSCs cannot be split into four separate channels since they are organized as two channels of quadrature decoder.
If the incoming pulse speed is not too high (< 200Hz) you may be able to define them as interrupt inputs and each of their associated ISR can be programmed to increment or decrement a variable, which serves as a counter for your program.
E.g. ISR for interrupt input #1 (rising edge) A = A + 1
ISR for interrupt input #2 (rising edge) B = B - 1
etc.