So the object of the script I\'m making is to compare files from two while read lists that have file path names in them...
while read compareFile <&3;
I think I would restructure that along these lines:
while true
do
read -u3 line1 || break
read -u4 line2 || break
# do whatever...
done 3< file1 4< file2
That uses a single loop, and will exit that loop when end of file is reached on either input file. The logic would be a little more complicated if you want to read both files entirely, even if one ends early...