hi all : 
 Best solution I found is to update configuration table directly

For example: you've added a new user variable called DummyVariable (Int32, initial value is 9999) into the existing pkg and want to use pkg configuration to make it dynamic (we use sql server table to store), If using the GUI, depending on your luck, sometimes, the GUI will hang while sometimes it won't . If it does end up hanging, the best solution is to update Configurations table directly

insert [SSISConfig].[dbo].[SSIS Configurations]
( [ConfigurationFilter]
     ,[ConfiguredValue]
     ,[PackagePath]
     ,[ConfiguredValueType])
     Values
    (
    N'DummyFile2',
    N'9999',
    N'\Package.Variables[User::DummyVariable].Properties[Value]',
    N'Int32'
    
    )

Of course, it comes with some manual process. However, if you got stuck with pkg deployment mode or still using SSIS pre 2012, this is your best bet. 

Cheers

 Hui