I'd collect the eggs, bath them in a meth blue solution, and place them to clean water container to hatch. (The reason for meth blue is to make sure you are not carrying the infection along with the eggs, it is effective against most bacterial pathogens in water, including flex.) The eggs you leave in the tank may be eaten by the cories, ditto for the fry, and those that survive may develop the disease... but removing and cleaning the eggs gives them a chance.
Incidentally, tetracycline is nearly a useless medication: most pathogenic bacteria is resistant to it now. If "mouth fungus" you are dealing with is flex, then the effective meds are kanamycin and/or furan.
Good luck!