QB Issue Resolution:

Run a customer balance report and see if there are balances for each, could be credits exist.

Resolution for Issue 'Customer merge does not seem to work in QB 2015' available: Yes (Solved).
Source: Intuit Community forum.

Customer merge does not seem to work in QB 2015: 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 Customer
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Error Recovery for Customer [Canada]
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