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Thanks for providing above details.

As per your current requirement I've modified script lit bit.

Now please check.

awk 'NR==FNR{A[$1,$2]++;...

Try

awk 'NR==FNR{A[$1,$2]++; B[$1,$2]=B[$1,$2]?B[$1,$2]<$3?$3:B[$1,$2]:$3;next}{if(A[$1,$2]>1){if(B[$1,$2]==$3){print}else{print > "another_file"}}else{print }}' file file

PS: Look the below code as written by an awk noob ;)

sort -k 1,2 file | awk '{print $1,$2}' | uniq -d > temp #Identifies the reduntant values and stores it in a temp file

while read i
do...

You did not specify what should happen
a) if the third column's values are identical
b) if values can go negative
c) to lines that do not have duplicates.
Thus any proposal might need further...