Check your DB. There is a table called
theme that stores a reference to all the themes that have ever been installed in your store. If the
type of the theme is set to 1, that means Magento sees the theme are virtual (what ever that means) and will no longer load your xml files. If that is the case, just change it to 0. I don’t know the why of this issue, but it has tripped me up a few time.