start:
23:55:00
01:00:00
01:30:00
02:30:00
05:30:00
23:00:00
end:
01:00:21
01:13:00
02:00:00
02:40:00
05:45:00
00:45:01

#!/usr/bin/somesh like bash or ksh
nextpart=0  # 1st/2nd section
while read line
do
        case "$line" in
                start*) cnt=0 ; continue ;;
                end*) nextpart=1 ; cnt2=0 ; continue ;;
        esac
        ((cnt+=1))
        
        # parse line to the array arr
        IFS=":" arr=($line)
        # start: section
        [ "$nextpart" = 0 ] && (( start[$cnt]=${arr[0]}*3600+${arr[1]}*60+${arr[2]} )) && continue
       
        # end: section
        ((cnt2+=1))
        (( end=${arr[0]}*3600+${arr[1]}*60+${arr[2]} ))
        starttime=${start[$cnt2]}

        # ex. start 23:xxx , end 01:00 , 24 h
        (( end < starttime )) && ((end=end+24*3600))
        ((diff=end-starttime ))

        (( h=diff/3600 ))
        (( m= (diff- h*3600 )/60 ))
        (( s= diff- h*3600 - m*60  ))

        (( h<10)) && h="0$h"
        (( m<10)) && m="0$m"
        (( s<10)) && s="0$s"
        echo "$h:$m:$s"

done < inputfile