I think I had a similar problem.First make sure you have wifi internet connection active or sync with cellular network "ticked" in iCloud "documents & data" page on your high level device (and kill an enemy) just to be sure you have the right save files in cloud.After that do this:
-Kill IB2 if its started
-disable "documents & data" sync and let it delete files from device (it wont delete from cloud)
-start IB2 and fight a bit (so it can create a new local save file) , after that kill IB2
-enable "document & data" sync again (dont forget your internet connection)
-Start IB2 , now it should replace the files from iCloud
Sorry for being so detailed ,I just want everything to be done right.Hope I helped

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