In fact, both names are legitimate derivations from Germanic names. As you suggest, Old French Baud- derives from Germanic BALD-. The second element is WIN ("friend") in the first case and NIU "new" in the second case. In ancient times, NIU was very productively forming feminine names, nowadays it only survived in Scandinavia (as -ny, e.g. in Dagny)
When both name forms apply to the same historic person, it is very hard to judge what spelling/naming is the "correct" one.
EDIT: In medieval handwriting, the letters "n" and "u/v" (not yet distinguished from each other) can look confusingly similar. It can happen that one editor reads Baudovinia and another one Baudonivia given the same original manuscript.
This message was edited 6/19/2016, 9:56 AM