Problem with Extended Capacity Drive

I am having a problem with an Extended Capacity drive (Seagate 3TB) being used as a data drive. I had the drive broken in to two MBR drives; the first 2 TB and a 768 GB for the remaining. My system drive recently had an issue where is started running in PIO mode. I uninstalled the Primary IDE device in Device Manager and after rebooting my system and the device re-installing the drive was correctly running in UltraDMA mode. However I lost my 768 GB data drive; the 2 TB portion is working fine. I am trying to be careful not to lose the data on the drive. If I use the Extended Capacity Manager to re-create the drive will I lose the data or should it still be there?

Thanks

Tim