If I cheated on my husband after we separated, what can he do to me in court?

Your husband is either wrong or simply trying to intimidate you.  In Georgia the rule for property division calls for "equitable dvision," which means that the property is to be divided "fairly" (what that actually means could fill a book, but that's the essence of it).  Commencing a relationship after you have been separated (or even before) will not mean that you have no claim to your fair share of the marital property.  Depending on the circumstances, adultery - if proven at trial - could affect any claim you may have to alimony.  But it is unlikely to have any effect on your property division, and certainly won't mean that he gets "100%".

Do not let your Husband intimidate you even through the last stages of your "married" life.  Do you have an attorney?  If you do, please confirm my understanding of the law in Georgia with him or her.  If you do not, then get one.

Generally speaking, if you have already filed for divorce you can not be considered an "adulterer."   Why?  Because the Courts can pin point a date certain that the marriage formally "ended" and that you are moving on as separate people. This can also be done through a formal separation agreement if your state allows or a settlement agreement signed by both parties.  Adulterer is also not a bar to your receipt of what is due you under the equitable distribution laws (for your assets).  It can be a factor in consideration of alimony and child custody (how it impacted on the children) but again, this is generally when it is raised as grounds for divorce.  If your husband can not prove that this affair happened before he left and has not sued under these grounds I really would not worry here.  Get help. Good luck.