We've never had that exact situation, but is the school saying that your DD's permanent school record won't include the new score? If it would just include both, I wouldn't worry too much about it (scores can dip and rise). If the school will ignore the first score in favor of the second, you probably shouldn't worry too much about them both appearing on the report. DD once had a pretty decent winter MAP drop (and they didn't do a retake, because it was still relatively high) that popped back up in the spring. DD had decided to stay up all night reading a book the night before winter MAP (unbeknownst to us until the next morning)...that score is still on her permanent record, but it has never hurt her.
