After getting over a bad Flu, can the Flu settle in your back for a while?

your question is very concerning!
You need to go back to a doctor to have your lungs checked, first, to make sure you haven't developed pneumonia, and also have your kidneys checked to make sure you haven't developed an infection. Your kidneys are in your middle-to-lower back, perhaps they are swollen. There are lots of other important organs that could hypothetically cause back pain. Go to your doctor if you think something like this is wrong!

in the meantime, body aches are a symptom of the flu, but they are usually spread throughout the body and not concentrated to one part of the body. Perhaps it's a sore muscle, a muscle cramp or spasm that's causing the pain. (perhaps from so much of staying in one position in bed or on the couch while being sick?) try a heat pack for five minutes at a time. (be careful not to leave it on the same spot for too long, as internal organs can only function at the normal 98-ish degrees.) If that doesn't start to relax the pain, try alternating a hot pack and a cold pack. If you've got access to a hot tub, I bet that would help out if it's muscle-related!

Good luck, and I urge you to go back to the doctor to make sure that nothing larger than the flu is going on here.