QB Issue Resolution:

There’s an ongoing issue with our Payments customers when a merchant deletes an item from the GoPayment app, it also deletes the item in POS loosing the whole item from the desktop app.

Our Product team is already aware of this and is now investigating the root cause. To receive an update about this, you can be added to the email list by calling our Product Support Team. Here’s how to contact them: QuickBooks Online Payments. Then, let them add you to Investigation No. 33428.

Resolution for Issue 'when I delete an item on the gopayment app, the next time I sync with the quick books POS system it deletes it from the server computer. This never happened before.' available: Yes (Solved).
Source: Intuit Community forum.

when I delete an item on the gopayment app, the next time I sync with the quick books POS system it deletes it from the server computer. This never happened before.: 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.

Support for Payment app
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Error Recovery for Payment app [Canada]
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