idbeholdME: You find the machete in level 4 and you need it to progress. So if you are in level 4, just look around.
If you are past that, write down the amount of ammo you have, use the weapon & ammo cheat (URGON_ELSA) and just shoot out the excess ammo until you are back at what you had before. Don't use the weapons you don't have yet until you find them when you are supposed to.
Try pressing 6 to see if Indy pulls it out anyway.
At worst, you could try restarting the game...
Never had a weapon disappear on me so just coming up with alernatives.