Your SSD is now the operating drive. Windows is installed on the C drive. So to open an Open Office document on another drive you'll have to install Open Office on the C (SSD) drive otherwise it doesn't have the information to read the document. Registry not correct. It should see photos and music folders though. If your second HDD is still a C:\ drive I'm surprised Windows boots correctly as having two bootable drives can cause conflict.
It's difficult to explain as you're using a secondary drive that had Windows installed. Any programs on the secondary drive won't work as not installed on the C:\ drive. Data folders you should be able to see and backup but no program will run from the secondary drive in this setup.