Can "was" occur twice, consecutively, in a sentence?

Your sentence, "But I guess all there was was such a big lie," is grammatically correct. The accuracy of your sentence can be demonstrated by manipulating the noun phrase (NP) in the middle of your sentence. The NP all there was can be replaced by it, which results in the following sentence.

But I guess it was such a big lie.

While your initial sentence may sound wrong due to a double word, the only issue is a clunky noun phrase. The structure of an NP is (compliment) + noun + (compliment), and it functions as a single noun. Therefore, the phrase can be readily replaced by a single pronoun, and the flow of your sentence is resolved.

Ultimately, the only issue is flow, and the usage of two, consecutive was is completely acceptable in this context.