My bitch has been losing discharge again, so took her to the vet, she scanned her again, came back and said there is no evidence of a pyo but she has a slight thickness of the lining of the womb. She has given her yet more antibiotics, her bloods came back normal, but she is really off her food. I don't know what to think. What exactly is this thickness? and what does it mean for her future? Will she have to be spayed? or can it be fixed?.

I don't know anything in general about a dog's reproductive system, but the lining of the womb is just the blood which a forming foetus will feed on for the first few weeks of life.
The thickness just probably means that she is accumulating a bit more blood than normal and needs to get rid of it somehow.
The lack of interest in food is definately due to the antibiotics. This is because antibiotics are not very good for the intestinal flora which decreases one's appetite. Try giving her some bio yoghourt with live cultures and that should help to settle her stomach discomfort.

Thanyou josefina.