I just had this problem, it occured after a mate borrowed my decks to try and get them to work with his Virtual DJ software. I actually found the solution so thought I'd post here for anyone else who encounters the same problem.
Nothing really "resets" when you do that, so I'm not sure if perhaps both players were set to the same number or AUTO, but you can connect them two-at-a-time, even after they've been used with Virtual DJ, and it will work.
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Disconnect the link cable from both decks and turn them off. Turn one of the decks on. Open rekordbox on your pc then connect the deck to the pc via the link cable. Wait about 20 seconds. The link window should appear at the bottom of rekordbox and the player ID should light on the deck. Now disconnect and repeat the process for the other deck. Now switch both decks off and THEN connect the 2 decks via link cable BEFORE switching them both on again. This process resets the link mode they are in.