Most likely the ph problem would have come from the water and not from the soil, the water you add would adjust the ph of the soil. But you may find that the soil is burning your babies as it probably very rich in nutrients, your babies would need no nutrients for at least their first two weeks of life and then when you do feed them you start off small and build up, so dependent on the age of your plants would you know if they can handle the soil. What you may find you have done is actually wash out some of the nutrients in the soil which would improve the conditions for young plants. I would still transplant out of the soil and get them into a neutral medium like rockwall cubes or coconut husk or some good soil, without added nutrients, to start with then these can be put into your nutrient rich soil later when the plants are more developed.
Obviously everything I have said may be wrong as I don't have all the details of your grow but these are things to keep in mind and are probable causes.