Will throwing up cause a saliva gland that was getting better, be worse again?

Maybe. If you have a saliva gland that is clogged or infected, vomitting can lodge a particle to re-lodge or make the gland over-active and cause a salive stone to move up the parotid tube and cause more problems.
Can get worse. I do not know that what type of problem u have in the salivary gland & in which salivary gland. In humans, there are 3 salivary glands. Vomiting, most of the time brings acid back to the throat and mouth. Saliva is usually inactivated by the acid quickly, resulting in decrease amount of saliva. Dryness of the throat and mouth, where salivary glands r present, can make the salivary gland worse.