Is prayer valid when one wipes over henna after having a minor ritual impurity and performing ablution, by analogy with wiping over the khuff?

The water in Wudu (ablution) must reach all parts of the skin and head. Thick henna prevents this, so it is not permissible to wipe over it. Wiping over a bag placed over it is even more impermissible. Therefore, what your mother did by wiping over the henna with a bag placed on it is incorrect, and she must make up the prayers she performed in this manner.