In my opinion, you will be fine. There are following reasons:
1-You have evidence documents to proof for your time you are on holiday. Although CO knows exactly how long you went oversea , from the time you submitted until they process, it takes more than a year so I think CO will not strict this.
2-You already applied and was consulted by agent, so do not worry. The application was done, just try to keep update your information that Immi needs, such as Notice of Assessment/Payment Summary and Superannuation report at end of financial year, updated contract for your rent (if have), PCC, AFP.
"To make sure 100%, do not hesitate to email or call to Immigration Department" They can give the advice.
Good luck mate