delayed final manuscript submission
These things are almost always at the discretion of the editor. If you notified him that you need more time, you are probably in the clear. But even if for some reason the manuscript database of the journal decides that you took more than 2 weeks and forces you to submit your revised paper as a new manuscript, the editor will still send it to the previous reviewers and treat it as if it was a revision. That's because any other course simply makes no sense from the perspective of the editor.

In other words, the worst that can happen is that the date of submission on the final, published version of the paper is the date when you submitted the revised version, rather than the original. There are likely very few cases where that actually makes a difference.

In summary: Don't worry too much about this technicality.