Soil pH does not heal itself.
Your meter depends on moisture for an accurate reading.
You need to fix the soil pH. Better still, scoop out the chunk that each seedling is in and repot into good soil-water in with water at pH 6.8-7.0 to make up for the fact that the chunk has 3.5- adjusting the pH is probably going to cause a TON of stress to the babies, and a repot is preferable in this situation.