My side baby hairs fell out during hair transplant, and are just starting to grow back. Will Minoxidil make them fall out again?

Minoxidil is generally used to grow hair.  It isn't used to make hair fall out.  There may be a few instances where some people experience temporary hair loss.  If this is a concern it is best to discuss and explore your options with your doctor.

posh_hills_123,Having miniaturized hairs fall out after treatment with Rogaine is a positive, since usually these hairs will eventually re-grow thicker caliber hairs. Shock loss from hair transplantation in the area will sometimes grow back. You left a question in another post stating that your doctor had prescribed a cortico-steroid cream. What is the reason for that? It is not possible to make recommendations with out the benefit of all the information.

Minoxidil will often produce baby fine hairs in the hairline and may help these hairs thicken a little bit. Typically, these baby fine hairs on the front and side are already miniaturized, and are less likely to grow back strong after surgery unless they were transplanted. 

These side hairs, if they fell out and you are talking about your temple peaks, may or may not come back.