I just tried opening some old Flash 5 and MX FLAs, in CS6, and it seems to open them ok. I can open them in CS3 as well, so I'm not sure why that would have not worked for you.
So, I would be hopeful that you can work with the files. One possible difficulty is that MX was ActionScript 1, and CS6 can only make AS2 and AS3 documents. But hopefully it will cope with AS1.
Oh well, I tought Flash MX 2004 was AS2.0 by default. I'll give it a try on CS6 anyway.
Thank you, best regards
MX 2004 is when AS2 was introduced. MX was the version before that.
My mistake, the project's on MX 2004 not MX. Didn't know there was a "MX" only version