Two Apple ID's, how do you manually control them when connecting an iPhone to a Mac so no apps are lost?

I have two Apple ID's one which has been previously used on an iPhone to purchase goods and another new one, when I connect my iPhone to my Mac I've been told by an Apple specialist that I will lose apps from the other ID but they informed me that there is a manual way to control this so nothing is lost, the specialist wasnt able to tell me how exactly to do this, due to a lack of knowledge about it as it was not her area of specialism, so she gave me an article about how to create an Apple ID but hasn't given me a way to manual control the accounts and apps so that nothing is lost