The scenes were left in, but the giant spider was instead recast as an unspecified species belong to the primitive spider suborder Mesothelae.
The correct classification was not made until Walking With Monsters was well into production, and the giant spider was left in and called "Mesothelae" instead of Megarachne.
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In fact, no spider that large has ever been found: at the time the series began production, the sea scorpion Megarachne had been mistakenly interpreted as a spider.