about system design direction:
First if there is no REAL need do not create 2 different apps one GWT and other iPhone
create one but well written GWT app. It will work off line no problem and will manage your data using HTML feature -- offline application cache
If it a must to create 2 separate apps
than at least save yourself effort and do not write server twice as if you go with standard GWT aproach you will almost sertanly fail to talk to server from stand alone app (it is zipped JSON over HTTP with some tricky headers...) or will write things twise so look in to the RestLet library it well supported by the GAE.
About the way to keep sync with offline / online switching:
There are several aproaches to consider and all of them are not perfect. So when you conseder yours think of what youser expects... Do not be Microsoft Word do not try to outsmart the user.
If there at least one scenario in the use cases that demand user intervention to merge changes (And there will be - take it to the bank) - than you will have implement UI for this - than there is a good reason to use it often - user will get used to it. it better than it will see it in a while since he started to use the app because a need fro it is rare because you implemented a super duper merging logic that asks user only in very special cases... Don't do it.
balance the effort. Because the mess that a bug in such code will introduce to user is much more painful than the benefit all together.
so the HOW:
The one way is the Do-UnDo way.
While off line - keep the log of actions user did on data in timed order user did them
as soon as you connected - send to server and execute them. Same from server to client.
Will work fine in most cases as long as you are not writing a Photoshop kind of software with huge amounts of data per operation. Also referred as Action Pattern by the GangOfFour.
Another way is a source control way. - Versions and may be even locks. very application dependent. DBMS internally some times use it for transactions implementations.
And there is always an option to be Read Only when Ofline :-)