I believe that there is a bug with the IAnnotation:SetLeaderAttachmentPointAtIndex method.
Here is a simple macro that just gets the existing arrow points and sets their position to their current position. Thus there should be no change to the note leaders. This works fine for one leader but seems to only move the first leader no mater what index you put in. Included is a test part and drawing with notes. Select a note and run the macro to test.  Has anyone run into this?

Dim swApp As SldWorks.SldWorks
Dim swModel As SldWorks.ModelDoc2

Sub main()
 
 Dim swSelMgr As SldWorks.SelectionMgr
 Dim swAnnot As SldWorks.Annotation
 Dim swNote As SldWorks.Note
 Dim status As Boolean
 
 Set swApp = Application.SldWorks
 Set swModel = swApp.ActiveDoc
 Set swSelMgr = swModel.SelectionManager
 
 Select Case swSelMgr.GetSelectedObjectType3(1, -1)
 Case SwConst.swSelectType_e.swSelNOTES
 Dim swDispData As SldWorks.DisplayData
 Dim vArrowPts As Variant
 Dim nLeaders As Integer
 Dim i As Integer
 
 'get the annotation
 Set swNote = swSelMgr.GetSelectedObject6(1, -1)
 Set swAnnot = swNote.GetAnnotation
 nLeaders = swAnnot.GetLeaderCount
 
 If swNote.IsAttached Then
 
 'Save the arrow points information
 Set swDispData = swAnnot.GetDisplayData
 Dim vArrows() As Variant
 ReDim vArrows(nLeaders - 1)
 For i = 0 To UBound(vArrows)
 vArrows(i) = swDispData.GetArrowHeadAtIndex(i)
 Next i

 're-position the arrows back to their original location
 For i = 0 To UBound(vArrows)
 vArrowPts = vArrows(i)
 Debug.Print ("leader " & CStr(i) & ": " & Format(vArrowPts(0), "####.####") & ", " & _
 Format(vArrowPts(1), "####.####") & ", " & _
 Format(vArrowPts(2), "####.####"))
 status = swAnnot.SetLeaderAttachmentPointAtIndex(CLng(i), vArrowPts(0), vArrowPts(1), vArrowPts(2))
 Debug.Print ("Status: " & CStr(status))
 swModel.EditRebuild3
 Next i
 End If
 Case Else
 'do nothing
 End Select

End Sub