#!/bin/ksh

while read LINE
do
        IFS="~"
        # Break into $1, $2, ... $N based on IFS
        set -- $LINE

        # More than 2 chunks means it found more than one ~
        if [ "$#" -gt 2 ]
        then
                VAR="${1}"
                #toss $1, $2 becomes $1, $3 becomes $2, etc.
                shift
                # IFS affects how $* expands.
                IFS=""
                echo "${VAR}~${*}"
        else
                # Print the unmodified line.  We don't need to delete anything.
                echo "$LINE"
        fi        
done

$ ./ifsplit.sh <<EOF
010000306551~IN ~N~ |WINDWARD PK|Alpharetta|
a~b~c~d~e
a
b
c~d

EOF
010000306551~IN N |WINDWARD PK|Alpharetta|
a~bcde
a
b
c~d
$

./ifsplit.sh < input > temp ; cat temp > input ; rm temp