There are a few versions of the script, none of them I found are the final cut of the movie as released in theater or VHS or DVD (I have seen all three versions). At the end, there's music playing (Charlie picks one of Maverick's favourite in the jukebox) then they see each other and talk, with the lines of dialog you mention. In the script I refer to, these are the lines found on the last page:
CHARLIE : They gave me the big option. Anywhere. I checked around. Found out the best of the best were all gonna' be back here. So
I took Perry's job.
MAVERICK : This could be a complicated engagement.
CHARLIE : I don't know. I've only done it twice.
MAVERICK : How'd you do?
CHARLIE : Crashed on the first one. I'll tell you tomorrow. But its looking good so far.
This (she leaves the words hanging) seems more (to me) of a dramatic-romantic part than her saying something as in the original script, because it goes back to their first meeting, in the bar (page 34).
CHARLOTTE : how'd you do?
MAVERICK (remembering) : Crashed and burned on the first one...
CHARLOTTE (looking up) : ...and the second one?
MAVERICK (wry smile) : I'll tell you tomorrow. But its looking
good so far.