$ more file
Wregister( 45676, 0)
Wregister( 55550, 1)
Wregister( 44000, 0)
FlipFlop( 2342, 2)
$ more file.sh 
#!/bin/sh

while read line; do
  echo "$line" | grep "^Wreg" >/dev/null 2>&1
  if [ "$?" -eq "0" ]; then
     val=`echo "$line" | sed 's/^Wregister*([ ]*\([0-9]*\),.*$/\1/'`
     hex=`echo "obase=16;ibase=10; $val" | bc`
     echo "$line" | sed "s/$val/$hex/"
  else
     echo "$line"
  fi
done < file

exit 0
$ chmod +x ./file.sh
$ ./file.sh > newfile
$ more newfile
Wregister( B26C, 0)
Wregister( D8FE, 1)
Wregister( ABE0, 0)
FlipFlop( 2342, 2)

BEGIN {
  FS="[(,]"
  OFS=","
}
$1 == "Wregister" {
  $1 = sprintf("%s(%X", $1, $2)
  $2=$3; NF--
}
1

BEGIN {
    for (i = 0; i < 10; i++)
      hex[i] = i
    hex["a"] = hex["A"] = 10
    hex["b"] = hex["B"] = 11
    hex["c"] = hex["C"] = 12
    hex["D"] = hex["d"] = 13
    hex["e"] = hex["E"] = 14
    hex["f"] = hex["F"] = 15
  }

  function dehex(h,  i,x) {
    for (i = 1; i <= length(h); i++)
      x = x*16 + hex[substr(h, i, 1)]
    return x
  }

{
 $2 = dehex($2)
 print
}