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The following diagnostic is generating: "Endng inventory in the COGS section is different than the ending inventory on the balance sheet." I input ending inventory in the COGS input screen, it auto populates the Balance Sheet. All good, except I have to effectively remove ending inventory and increase COGS in order for it to calculate correctly on form 1125-A.
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S-Corp module, Screen 14? My workaround for that is to re-input beg & ending inventory in Screen 14 (as well as the balance sheet).  Then in "Purchases", I create a table with CTRL+E.  I line item: 1) COGS from my P&L, 2) Add: Ending inventory, 3) Subtract: Beginning Inventory.

That makes sense, good idea!  I was basically doing the same thing, except not utilizing purchases to show the calculation of capitalized inventory.  I did not also enter in depreciation (screen 14 for partnerships) as I see no need.  Ending inventory and COGS agree, and my balance sheet is in balance.  Thank you for your advice!

Susan