Thank you for your query and the detailed description of the illness.
Without having a look at the lesions it is not possible for me to give you the likely cause of the problems that your daughters are experiencing. However, the conditions that you mentioned have the following features:
1. Herpangia: presents with fever
and sore throat
. The lesions are in the back area of the mouth
2. Hand, foot and mouth disease: lesions should have been present on the peripheries of the limbs
Simplex: the lesion is usually painful and fever is not a feature of it
As your elder daughter had a history of cold sore
the problem could be an infected Herpes Simplex infection which started resolving after you gave her antibiotic. However it is difficult to say that your younger daughter is having the same infection as I mentioned earlier that Herpes Simplex is usually not associated with fever.
The best course would be to do a detailed investigations including viral studies.
I hope I have answered your query to your satisfaction.
Wishing your daughters an early recovery.