Unfortunately this is a FP (False Positive), which means Avast! is wrongly detecting a valid Windows' system file as a virus/trojan. Best course of action is not to do ANYTHING and wait for a new VPS (Virus definitions file) to be released that deals with the issue.
Atapi.sys is a Windows system file that deals with input/output access to devices (harddisks, cdroms, etc) that comply with such an interface (connector type and data bus). It is not a file that can be targeted for virus/malware infection since it is always in use and its deletion or modification leads to system unstability or unuseability which would essentially negate the purpose of the trojan or virus, which is either theft or to spread.
Since one of your HDDs has "disappeared", I'd advice to perform a system restore so that the earlier settings are recovered. Once you recover, if Avast! nags about atapi.sys being infected, click on "ignore" or "do nothing" until the alert goes away & wait for the VPS update.
Best of luck.