#!/bin/bash
s='>AX-89916436-Affx-G-[A/G]
XXXXXXX
>AX-89916437-Affx-A-[A/G]
XXXXXXXXXXX
>AX-89916438-Affx-C-[A/C]
XXXXXXX
>AX-89916440-Affx-T-[G/T]
XXXXXXX'

awk 'BEGIN{FS=OFS="-"} /^>/ && $5 ~ /\[[A-Z]\/[A-Z]]/{gsub("[][/"$4"]", "", $5);}1' <<< "$s"