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In Game Courier, at least, the FEN code and the move notation are in
separate fields. So the use of - for moves does not affect the use of - to
represent spaces not on the board.

GAME Courier used to pass FEN code representing the current state of the
board with each move. This was before I implemented log files and the use
of GAME Code for enforcing rules. Now the only FEN code it uses is for the
opening position. Each time a player moves, it goes through all the moves
in the game, updating the board, which is held in an array, with each
move. If there is code for enforcing rules, it also checks the legality of
all previous moves. Finally, it gets to the last move, finishes updating
the board, and displays the current position to the player.

One reason I made this change is that it allows Game Courier to use
relevant information about past moves to tell whether subsequent moves are
legal. In Chess, this is important for castling and en passant. You can't
tell from FEN code alone whether a King can castle or a Pawn can perform
en passant. It might be possible to overload FEN with this kind of
information, but I didn't think it would translate well to games that
either didn't need it or had different rules concerning how past moves
affect the legality of present moves. Rather than trying to anticipate all
possibilities of this sort in an expanded FEN standard, I left it to GAME
Code to keep track of it by using flags or variables.