Your question is about what auditors do and a legal question about what they are allowed to do. It may be off-topic for superuser.com.
I don't know what AutoDesk will do, but they can only do what you agree to. When you install most software packages, they typically display a licence agreement and ask you to read it and agree to it. That agreement sets out what you have agreed to allow Autodesk to do.
Most likely, AutoCad has "phoned home" to register the new installation and AutoDesk have detected that your licence has already been used on a different computer. They just want to reassure themselves that you are not in breach of licence by using one licence on multiple computers.
Since anyone could write to you purporting to be Autodesk you are entitled to verify the validity of the letter independently - for example by looking up the support phone number for autodesk and phoning them (or emailing them) and asking for confirmation of the contents of the letter. You could also ask them what exactly they propose. If in doubt get legal advice from a qualified lawyer.
The outcome of an audit may depend, in part at least, on what happened to the drive you replaced, if someone else is now using it and can run your original installation of AutoCad then you could be deemed to be in breach of the licence.
If so, Autodesk might demand you purchase additional licences.
If you are unable to agree with them, Autodesk might terminate your licence agreement - you might then have to look for a replacement product.
The worst case is that AutoDesk might go to the courts and seek financial damages and/or punitive fines. I think this outcome is unlikely, but that is just my personal, non-legal opinion.