If you have only been editing the same window, you will receive this message as the GUID for the window will not have changed. To get around this I generally copy the original window (prior to making changes to it) and call it version 2 (or v2) etc, which creates a new window with a new GUID. That way when you do you design transfer, the window goes across fine as the GUID does not exist for this one.
Just remember to update any applicable view rules after this.
Pauls method is the best in terms of moving across just what you know you have modified and is highly recommenced. You can also apply it to queries, processes and so on. You could also take a look at the following utility which might prove to be a useful alternative.
Be aware though that this utility transfers across everything you have done (including any 'test' items you have created and left in place). You'd also need to have had your PROD and TEST environments be exactly the same by a database refresh before you started your mods.