If you want to express the idea that you took a very meaningful trip, which enabled you to see many wonders on the island, then the verb should be in singular. Throughout the two-day trip we saw many wonders on the island that we had never witnessed before and that was very meaningful. But if you want to say that the wonders were very meaningful then the sentence needs rephrasing: Throughout the two-day trip we saw many wonders on the island that were very meaningful, which we had never witnessed before.
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