I'm able to go and change my database alias path with no problem using:
  slMy :=TStringList.Create;
  slMy.Clear;
  slMy.Add('Path='+'D:\MyDirectory\XtraDir');
  Session.ModifyAlias('MY_DATABASE', slMy); //Now change the Path
  slMy.Free;
  Session.SaveConfigFile;  //Makes alias modification permanent by saving to
IDAPI.cfg file

Except after I have created a table:
    Table1.CreateTable;
Once I do that I can no longer change my alias path.  (it thinks that I am
always working in the directory where the Newly created table exist).  When
I view the DatabaseAdministrator it show the desired directory.  But it is
as though the Table doesn't know that there is a new database directory.
I can change the table name though:
      Table1.TableName := 'NewTableName';