It wouldn't be a case of association. If it was, they would still be visible in "my computer" and the format prompt would not be displayed. The PC thinks the card is corrupt. There is software to recover at this stage, but would still result in having to format the card at some stage. It won't be possible to read/write anything until the PC thinks it is ok.
Do the games work when you put the card back in the DS. (I am not asking if they did work.) If you have copies of the game on HDD, it is simpler to format it and start again.