@Simon > Sorry to hear about that failed hard drive - I had the same experience only this week on a 6mth old MacBook Pro.
Where you able to recover anything from it or is it totally dead?
The best solution I can think of is you drag your music back on to your new hard drive and then import it into Rekordbox. Let Rekordbox analyze all the tracks again etc. Then plug in your SD card and select the tracks with the hot cues / loops set etc. Right click (PC) on those tracks on the device and then select 'Update Collection'.
If you do have all the database files saved, I do believe you could load them onto your new hard drive and then point rekordbox to look there for the data.
This thread might be of use to you: http://forums.pioneerdj.com/entries/20658308-migrating-your-rekordbox-database
As you can see, there is a change in the path structure from one OS to the next.