M.F.
Apparently the scare has to do with isoflavones in soy.
http://www.healingdaily.com/detoxification-diet/soy.htm
However, the reason you might want to switch back to the soy formula is because regular soy milk doesn't have much, if any, fat in it. Toddlers need the fat for their brain development.
For this reason, we put our daughter on goat's milk from age 1 to 2, then switched her to regular soy milk (actually, the Silk brand Very Vanilla). With our son, in whom we also suspected a milk allergy, we simply kept him on soy formula until close to his 2nd birthday, then started giving him the same soy milk as his sister.