#! /bin/ksh
i=0
for list in `ls -l file*`
do
if [ $i -lt 99 ]
then
tmp=`echo $list| sed "s/^[a-z]*[0-9]*$/flat$i/"`
mv path_to_dir/$i path_to_dir/$tmp
i=$((i+1)) ;
fi
tmp=`echo $list| "sed s/^\([a-z]\)\([0-9]*\)/flat\2/"`
mv path_to_dir/$i path_to_dir/$tmp
done < /tmp/files.txt


( not tested )