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As was pointed out, the depreciation a taxpayer is eligible to take lowers the Basis, regardless if they actually took it or not. So the taxpayer has a gain from the sale.
However, Form 3115 can be used to 'catch up' on the missed depreciation. Although the usual rule for Form 3115 is that is must be on an original, timely filed tax return, this specific change (change 107, in Section 6.17, for disposed property) is allowed on an amended return. So that will allow that full deduction (the deduction will be 'ordinary' rather than 'capital', which works out good for your client).
(3) Manner of making the change.
(a) Change made on an original return for the year of change. This change may be made on a taxpayer’s timely filed (including any extension) original federal tax return for the year of change (as defined in section 6.17(4) of this revenue procedure), provided the taxpayer files the original Form 3115 in accordance with section 6.03(1)(a) of Rev. Proc. 2015–13, 2015–5 I.R.B. 419.
(b) Change made on an amended return for the year of change. This change may also be made on an amended federal tax return for the year of change (as defined in section 6.17(4) of this revenue procedure), provided:
(i) the taxpayer files the original Form 3115 with the taxpayer’s amended federal tax return for the year of change (as defined in section 6.17(4) of this revenue procedure) prior to the expiration of the period of limitation for assessment under § 6501(a) for the taxable year in which the item of depreciable or amortizable property was disposed of by the taxpayer; and
(ii) the taxpayer’s amended federal tax return for the year of change (as defined in section 6.17(4) of this revenue procedure) includes the adjustments to taxable income and any collateral adjustments to taxable income or tax liability (for example, adjustments to the amount or character of the gain or loss of the disposed depreciable or amortizable property) resulting from the change in method of accounting for depreciation made by the taxpayer under this section 6.17.
