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.
As Anna pointed out, cash payments are allowed. Although sometimes difficult to prove, it seems like the contractor is willing to help, so that should clear that up. If the auditor still has a problem with that, you may need to request their supervisor. Make sure the client knows that for any future businesses that payments should be by check and be connected to an invoice.
As for the other deductions that the auditor is claiming might be personal, can you show how those items would likely be used in the taxpayer's line of business? If so, I would ask the auditor why he thinks they are personal, when that type of item is used for that type of business. Personally, I am stubborn with that type of thing, and would insist on the auditor allowing those deductions (or appeal, or go to Tax Court).