QB Issue Resolution:

use make deposits, at the bottom is cash back, select the merchant fee expense account and enter the fee amount, when you click out of that block QB should show the correct deposit amount

Resolution for Issue 'how do I make deposits from undeposited funds for merch settlement' available: Yes (Solved).
Source: Intuit Community forum.

how do I make deposits from undeposited funds for merch settlement: 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 correct deposit amount
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Error Recovery for correct deposit amount [Canada]
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