Can switching soy base formula to regular milk base, harm by 3month old baby? if babies stay on soy base, will that effect her when she gets older?

Varies: There are babies that are intolerant to milk based formulas, either to the protein or the lactose sugar. These kids will be chronically fussy, have acidic stools or otherwise a mess. If your kid can eat, digest and act comfortable on a milk based formula it is ok to switch. You might want to review the idea with the doc, some use soy for kids with galactosemia and a change to could be harmful.