Given that you have a Reactive Form already in the template, I am not sure why this input isn't also a part of it. Then you could use something like the form group's valueChanges observable to listen to it's events.

Being said that, there are multiple quick fixes you could try.

Option 1: template reference variable

You could use a template reference variable in the <input> element and capture it's checked property in the event handler's argument.

<input type="checkbox" #inputBox (change)="onChange(employee?.id, inputBox?.checked)">

Here the #inputBox is the template reference variable.

Option 2: disable type checking

You could disable type checking using $any() function in the template.

<input type="checkbox" (change)="onChange(employee?.id, $any($event.target)?.checked)">

The safe navigation operator ?. is used to avoid potential possibly undefined errors.

Update: working example

Working example: Stackblitz

$event.target is of generic type EventTarget. TypeScript is not smart enough to recognize that the event would be triggered by the input and the actual type would be HTMLInputElement. You can do such a change to overcome it:

<td><input type="checkbox" (change)="onChange(employee.id, $event.target)"></td>

onChange(id: any, target: EventTarget | null) {
    const input = target as HTMLInputElement;
    const idFormArray = <FormArray>this.myForm.controls.employeeRelatedId;

    if (input.checked) {
      idFormArray.push(new FormControl(id));
    } else {
      let index = idFormArray.controls.findIndex(x => x.value == id)
      idFormArray.removeAt(index);
    }
  }