I'm not sure if you've seen what the coursework section looks like on OptomCAS, but when you enter a course you can give it a special classification - i.e. if it's been taken online, repeated, etc. You also list courses according to the semester/year you've taken them in, so if you redo a class you still have to enter it in twice in the coursework section regardless of whether its included in your gpa.
Are you re-taking these classes at the same university? Because when you send in your transcripts, they should also list the courses you're currently enrolled in (but are in progress). List your old grades in the year you took them and give them credit. Then list the new grades in the semester/year you are going to take them but classify them as "repeated" (if they're repeated at the same school), and then I guess you'd list them as incomplete (im not totally sure about that, check it).
Then in dec/jan you can send in an updated transcript, and change your old bad grades to have 0 credit (so they don't get calculated into your gpa), and then list the new grades.