Yeah, I did my whole chemistry a level together with my other a2 exams. You'll just get a predicted grade like you will for your other subjects (you'll probably have to persuade your teacher to give you a good prediction), and on your ucas app you'll just write the AS grades as pending along with your A2 exams for the AS exams you'll retake
I think it depends on your school/college. Our school allows you to carry on with E's but they do warn that the A2 material is harder than AS and with an E it might be a struggle. I would suggest you ask one of the advice people when you go back to see what the rules are at your particular institution.