Do you know why there was a System Reserved partition on the secondary HD which you say you use for data?
Deleting it should not affect access to the data at all.
Please post back a screenshot of your maximized Disk management drive map with listings, using Snipping Tool in Start Menu.
You can rescue data that is stranded using the Windows 7 DVD or System Repair Disk: Copy & Paste - in Windows Recovery Console
to external or the primary HD. Or use Paragon rescue disk; recover data.
Then wipe the HD to clear possible boot sector code with Diskpart Clean Command
, repartition in Disk Mgmt.