The only 2 issues I've had is some reports can look a little wonky if you create them in one interface and view them in another. It's not that they were unusable, just some weird column widths and UI stuff. To be safer, I would take a quick peek at all your reports in both first. Also, URLs are sometimes different in each interface. If you copy and paste a URL to someone for a specific page, it may or may not work.
