QB Issue Resolution:

A clarification – ‘Order cost’ does nothing. Average cost – or sometimes just listed as cost is your cost field. When you imported owned qty you also needed to import your current average unit cost. Since you didn’t your inventory had no cost.

Beyond that yes, a export import will be the fastest way to fill in cost as Banks Suggested. In cases where your cost is still 0 somehow just move your order cost over to cost. in cases where you do have a cost and it is different than your average you will just have to try to figure those out.

If you use QuickBooks with your POS maybe you can do some adjusting with an accountant (placing in your inventory value from your original import spreadsheet if you have it) to make things look right in Quickbooks side PNL. Talk with your accountant they may have better ideas.

Resolution for Issue 'POS thinks I didn’t pay for my initial inventory, and all EOY reports list the “ext cost” as zero. This is messing with my margins and COGS. Help!' available: Yes (Solved).
Source: Intuit Community forum.

POS thinks I didn’t pay for my initial inventory, and all EOY reports list the “ext cost” as zero. This is messing with my margins and COGS. Help!: this issue or error code is a known issue in Quickbooks Online (QBO) and/or Quickbooks. Support for this issue is available either by self-service or paid support options. Experts are available to resolve your Quickbooks issue to ensure minimal downtime and continue running your business. First try to resolve the issue yourself by looking for a resolution described below. If it is a complex issue or you are unable to solve the issue, you may contact us by clicking here or by using other support options.

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