This would be better asked in the Crystal Enterprise forum.
My first thought is that BOE 4 introduced universes built with the Information Design Tool (.blx). Universes built using the Designer (.unv) are still supported, but you may be trying to import a new IDT universe into the old universe Designer. Try importing using the IDT.
Also, the Webi documents might be using a cached version of the universe which is why it still works. Do you have a local copy of the universe stored somewhere? If not, I would check the cache folder which is usually located here:
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