You HAVE to put your previously achieved grades - unless you resit the exact same subjects/ exam boards. Even then, there may be a section requiring the dates you were enrolled at college or something, I can't quite remember...
They would probably ask what you were doing during you supposed two year break between GCSEs and A levels - it would be very unusual. They would expect you to either have some medical reason not to continue at college, have had a full-time job (which they may be suspicious of, medicine is a very tough degree - taking a break after GCSEs may suggest you were less keen on studying), have done lots of work experience or something. If you just leave those years suspiciously blank they will think you either failed A levels, or sat around at home watching TV.
Bear in mind that you will have to pay for sixth form if you will be over 19 (18?) when doing your A levels - it is not covered by the government I don't think. However, if you resit your AS year now and continue on to A2s you should be fine - although you will probably struggle applying to medicine. Perhaps consider related courses such as biomedical sciences, and if you are still interested in medicine you can apply for graduate entry?