How/where do you think your code handles the case of missing data?

I suggest that you add print statements to every line to see where your program progresses.

Especially add print statements to the cases where valid data is found and where missing data is handled:

...
if (defined  ($eSheet->{Cells}[$row][0] ))
{
    $master_key=($eSheet->{Cells}[$row][0]->Value);
    $r=$row;
    print "Found (new) master key '$master_key' in row $r\n";
}
else
{
    $master_key=$master_key;
    print "No (new) master key found in row $row, keeping current mast
+er key '$master_key' from row $r\n";
}
...
if (defined $eSheet->{Cells}[$row][$col])
{

 $val=($eSheet->{Cells}[$row][$col]->Value);
 print "Found valid value for '$key' in ($row,$col): '$val'\n";

}
else 
{

 $val=$eSheet->{Cells}[$r][$col]->Value;
 print "Found invalid/empty value for '$key' in ($row,$col), reusing t
+he value from ($r,$col): '$val'\n";

}
[download]

Also, your code would greatly benefit from indenting every line by four spacess for every level of nesting. This makes it much easier for you and others to recognize the structure. Instead of

foreach $row( 1 .. $eSheet->{MaxRow} )
{
if (defined  ($eSheet->{Cells}[$row][0] ))
{
$master_key=($eSheet->{Cells}[$row][0]->Value);
$r=$row;
}
else
{
$master_key=$master_key;
}
...
[download]

write the code as

foreach $row( 1 .. $eSheet->{MaxRow} )
{
    if (defined  ($eSheet->{Cells}[$row][0] ))
    {
        $master_key=($eSheet->{Cells}[$row][0]->Value);
        $r=$row;
    }
    else
    {
        $master_key=$master_key;
    }
[download]

Also see perlstyle and perltidy.