I am more concerned about why you have some left in the medicine cabinet! When given this drug it is important to finish the whole course.
Amoxycillin is a broad spectrum penicillin whereas E-mycin (recommended for cyano) is an antibacterial, macrolide. I do not know enough about them to advise but wonder if the Augmentin may attack other types of bacteria and so also kill off the good filter bacteria and maybe/or maybe not the cyano. Sorry I can't help at the moment but, once I find out a bit more about cyano I will ask my medical friends (they will need to know more about the cyano before they advise) and get back to you.