"Who would've thought that working with you would have been a silver lining?" Actually, I don't quite understand the usage of "would have been"? What's the difference if I replace "would have been" with "was"?
The implication that user3847720’s answer mentions is already made with the beginning of the sentence, "Who would've thought." The second instance of "would have" does nothing to emphasize this.
Using was instead of would have been feels awkward here because you're moving into past tense. But the original version feels awkward because they've used a contraction of would and have at the start of the sentence, and then used those same two words later on in the same sentence, so neither is a good option.
"Who would've thought there would be a silver lining to working with you."
This seems the best choice to me. Essentially the use of would have been here is redundant, and replacing it with was doesn't work.