Your photos are not "IN" Lightroom.
Your photos remain on your hard-drive. (So DO NOT DELETE THEM!)
Lightroom only creates a database (catalog) of previews to show your photos on your hard-drive.
If you right-click a photo in the Library Grid of Lightroom you can see where that photo is on your hard-drive by selecting- "Show in Explorer/Finder"
It is possible you did a "Copy into one folder." when you "Imported" previews- then your photos may be in TWO places on your hard-drive.
Upgrading the LR3 catalog to LR5 should not have changed anything re your catalog and photos.