The actual question I see here is that will there be any loss of data or functionalities or code from the already present 2003 format excel files........ If this is the question... the answer is the office 2007 and 2010 supports the 2003 format data very well.... You might face some difference...
what Yard has specied is the best way. But in your case the formulae should be
=IF(COUNTIF($A$1:A1,A2),"",A2)
use this in a blank column on row 2 and drag it to the end of your data.