A VBA script that will reconcile the version without locking the parent.

NonLockingReconcile.vb

' Reference Miner & Miner 9.x Geodatabase Library

Sub NonLockingReconcile()

On Error GoTo ErrorHandler

  Dim conflictWindow As IConflictsWindow3
  Dim editor As IEditor
  Dim editorID As New UID
  Dim conflictID As New UID
  Dim hasConflict As Boolean
  Dim workspace As IWorkspace
  Dim version As IVersion
  Dim versionEdit As IVersionEdit4
  Dim versionInfo As IVersionInfo
  
  conflictID = "esriEditor.ConflictsWindow"
  editorID = "esriEditor.Editor"
  
  Set editor = Application.FindExtensionByCLSID(editorID)
  Set conflictWindow = editor.FindExtension(conflictID)

  If (editor.EditState <> esriStateEditing) Then
    MsgBox "You must be editing to reconcile."
    Exit Sub
  End If
  
  Dim au As IMMAutoUpdater
  Set au = New MMAutoUpdater
  au.AutoUpdaterMode = mmAUMNoEvents
    
  Set workspace = editor.EditWorkspace
  Set version = workspace
  Set versionEdit = workspace
  Set versionInfo = version.versionInfo

  hasConflict = versionEdit.Reconcile4(versionInfo.Parent.VersionName, False, False, True, True)
  
  If (hasConflict) Then
    conflictWindow.Visible = True
    conflictWindow.Reset
  Else
   MsgBox "Reconcile completed."
  End If
        
  Exit Sub

ErrorHandler:
    MsgBox Err.Description
End Sub