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 Win7 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.