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It says in codex space marines they where destroyed by the necrons but in the chaos codex its says they where pulled apart and destroyed by chaos.
So what accentually happened to them?

They are two seperate chapters as the events of each chapters destuction are over one millenia apart.

If however they are ment to be the same chapter and it is a rewrite then C:SM is canon as it is newer than the C:CSM where the fluff came from

Oh didn't no that thorght that they where the same chapter!

Its possible that the chapter got destroyed at one point and then was re-founded using the gene seed stocks each chapter is required to send to mars in case of such an event, so its possible that the same chapter has been made extinct twice.

Now that's just unlucky... though the Alpha Legion's attack was a work of art so go figure.