The flaws on using traditional EV is well known and documented, it has been suggested to update its use with the concept of an extension known as Earned Schedule.
From:
http://www.pmforum.org/library/second-edition/2011/PDFs/jan/SE-LIPKE.pdf
"The analysis indicates that the aberrant behavior of the EVM schedule indicators, SV and SPI, is overcome by employing the Earned Schedule (ES) computation methods. The application of Earned Schedule provides a set of schedule indicators, which behave correctly over the entire period of project performance."
I believe no method is perfect because there is no way to know the future, you can only forecast based on a set of assumptions, even probabilistic methods are just predictions whose predictions shall be updated continuously. Any method that is based on a fixed baseline is wrong.
If you look at my previous posting you will see two independent Banana Curves, one based on a Baseline perhaps an already obsolete baseline or an updated baseline and another set based on actual predictions using the updated schedule. In order to know where you are in comparison to original plan you must show all three banana curves, at minimum. I would say you should compare preferably in two separate diagrams the progress of your job. One diagram displaying the original baseline banana curves versus actual baseline and another comparing latest updated schedule banana curve against current/revised contractual baseline. Everyone knows the data displayed by S Curves is somewhat limited, just a birds-eye view and as such shall be interpreted, as something subject to change, as something dynamic.
Good management practice requires for the documentation and analysis of changes, it starts after your updates, it do not ends there.