QB Issue Resolution:

There isn’t a way to delete it as now it is in use.  It’s actually important to use it, in case it ever applies to any employee later in the year, and for reporting purposes.

Resolution for Issue 'delete medicare employee additional tax' available: Yes (Solved).
Source: Intuit Community forum.

delete medicare employee additional tax: 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 applies to any employee
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Error Recovery for applies to any employee [Canada]
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