The reason for spaces being skipped is in your line

@array_A1= split (/$column_separator/,"$columns[$column_number]");
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If $columns[$column_number] is the empty string (not " " but ""), then your split will return an empty array, ie you lose your blank cell you are looking for.

I would think instead of

@array_A1= split (/$column_separator/,"$columns[$column_number]");   
@array_A2=@array_A2,@array_A1);
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you should just do

push @array_A2, $columns[$column_number];
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I assume the exit statement is left from debugging but it will stop execution of the script immediately which makes no sense at this point.