If you mean the saves are nowhere to be seen in the game load save page but are still viewable in MyDocs\SH3.....add an 'x' to the career and they should reappear.
If that is in fact not the case, make a backup of your saved folder (as already suggested) and add the 'x' anyway as a future precautionary error.
I have often experienced the first problem, but never the dissapearance of both (in game and MyDocs)
