Meaning of 'not under active consideration' in APS peer review process
The APS system does not set a deadline for the authors to submit a revised manuscript.  However, after a certain length of time (I believe it is about one year), a paper is automatically moved from "with authors" to the "not under active consideration" category.  That is the same category used for papers that have been outright rejected, but categorical rejections from Physical Review journals are relatively rare.  The letter your received, inviting you to resubmit if you feel you can overcome the referees' criticisms, is boilerplate, sent out in the response to every letter that the reviewers offer mild rejection recommendations for.

So you can resubmit the paper, although processing will probably be a bit slower than it might be otherwise.  The editor will try to send the paper back the same referees, and they may not have have the clearest memories of your manuscript after all this time.  They may not want to review it again at all, which will delay the whole process.