Hi and welcome to JustAnswer:
Your accountant is correct. In the year of the sale you must report as income the amount of depreciation recapture on the equipment. This is true regardless of whether the sale was paid in full or no payments were received. Details in Publication 537.
You will not be taxed twice. See page 12 of IRS Publication 537. It explains the process if personal property sold on an installment sate is repossessed. (Link below).
Hi Zeke -
Only the ordinary income must be reported in the year of sale (depreciation recapture). The amount that is allocated to goodwill will be reported on the installment basis and will be taxed at long term capital gains tax rates, currently 15% federal.
Hi Greg -
The ordinary income portion of the gain will be reported on the return in the year of the sale. You will be taxed on that portion in that year. If you are unable to fully pay the tax, you should be able to set up an installment payment plan with the IRS. Late payment penalties and interest continue to accrue on the unpaid balance while you make the payments.
Did you contact your accountant before you structured the deal?