Look at it this way,
A--------------------------------------------------------------------------------------> EM rules statement on how to treat EM tokens
B------------------------------------------ Physical EM card on the ship
C C Boba Fetting
At time point C, you discard the EM card. However, there is no timing window to check for how the tokens work again- it was a statement at setup. The only timing on how the tokens work (If they are still available at point C) is at setup. There is not another check on the EM card during the game.
I don't understand what you mean 'check on the EM card'. EM gives you the ability to equip and use ordnance tokens. Once the card is gone, you lose these abilities, just like with other upgrade cards in the game.
Edited by Ubul