From what I recall, DC was toying with some pretty significant changes to the character. Essentially it took them a while to figure out they wanted to do something more safe and traditional with Perez. And ... Donna just fell through the cracks so DC just threw it to Perez to try and fix.
Remember "History of the DC Universe" that happened shortly after COIE? The book that was supposed to answer all the questions left by the event but just ended up introducing a bunch of confusion? Good times.