Here’s one way to generate a set of commands with awk, and then run them in a loop with eval.

# cat snippet
field1 /mnt/somedir/785/8785/948785 41 /mnt/somedir2/785/8785/948785 1 2
field1 /mnt/somedir/791/8791/948791 2 /mnt/somedir2/791/8791/948791 6 2
field1 /mnt/somedir/924/8924/948924 2 /mnt/somedir2/924/8924/948924 23 2
field1 /mnt/somedir/993/8993/948993 2 /mnt/somedir2/993/8993/948993 19876 2
field1 /mnt/somedir/3/9003/949003 8 /mnt/somedir2/3/9003/949003 273 2
field1 /mnt/somedir/70/9070/949070 341 /mnt/somedir2/70/9070/949070 6 2
field1 /mnt/somedir/517/4517/954517 2 /mnt/somedir2/517/4517/954517 14 2
field1 /mnt/somedir/699/4699/954699 210 /mnt/somedir2/699/4699/954699 1 2
field1 /mnt/somedir/726/4726/954726 1 /mnt/somedir2/726/4726/954726 6 2

Now use awk to get the output you want and generate commands. Use a forloop and eval to run them.

# for i in `awk '{if($3>$5) print "rsync -a --ignore-existing "$2"/ "$4}' left.compare.sorted  `; do echo $i; eval $i; done;
rsync -a --ignore-existing /mnt/somedir/70/9070/949070/ /mnt/somedir2/70/9070/949070
rsync -a --ignore-existing /mnt/somedir/699/4699/954699/ /mnt/somedir2/699/4699/954699
#