Can I delete Employees from a cloned scenario without affecting the original?

The short answer is yes you can.

When you clone a scenario, you create a new version that is completely separate from the original. There are no links, so any changes you make in the clone will not affect the scenario you cloned from.

The Employee Module itself is unique to the scenario in which it lives, so you can have a completely different group of employees and HR formulas in each scenario if necessary.