QB Issue Resolution:

What you could do is setup a liability account in QB to track the loan you have with Shopkeep.  When you get a deposit from Shopkeep, enter the FULL amount of the deposit before the loan payment they remove and on the deposit, add a second line with a NEGATIVE amount for the loan payment and offset the liability account you created.  This way it shows you had correct income, but you had to use some of the deposit to pay the loan.

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Resolution for Issue 'How to record loan payments' available: Yes (Solved).
Source: Intuit Community forum.

How to record loan payments: 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 Income
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Error Recovery for Income [Canada]
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