Is it ok to put acrylic nails back on after mold set in under my last set? I had about 2 fills with my last set & since I had color for the last fill I didn't notice water getting under the acrylic on my thumb. He cleaned it with alcohol I believe. 

Alcohol will not kill nail fungus or mold, as you described it.  It
would be important to leave the acrylics off until your nails grow out
and the mold is gone. You might want to purchase a nail fungus
solution, as well, and apply it according to directions.  I would not
recommend covering up your nails with acrylics until your nails are
healthy again.