Where exactly did you get the idea that they'd lost them?
The solicit for the last issue of the Spirit ongoing make an oblique reference to First Wave ('but stay tuned for a radical reinvention that will leave you breathless!'), so it's pretty clear there was no loss of rights involved in ending the series.
Either the sales tanked (and I can believe it - I dropped it early in Evanier and Argones run), or they dropped enough that DC thought it was worth keeping only the First Wave version around.