In determining gross income for the filing requirement, gains but not losses are used in that determination. It is not the proceeds, but the gain that is taken into consideration. That being said, even when the basis is reported to IRS and no gain exists, the AUR will be using the sale side only and this new client may receive a CP2000 in about 18 months.
You should explain the filing requirement to the client, and personally I'd advise this client to file a return to avoid the notice. Even without an extension, there shouldn't be any penalties assessed since no tax is due and the client doesn't actually have a filing requirement. If penalties are assessed, those should be easily explained and abatement requested. Filing also establishes the statute of limitations date in the event that you are missing some piece of income from this new the client.
What about a state filing requirement?