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Didn't people who work at the facility say "flooding" was an exaggeration of what actually went down?

Yes, it was a leakage, not flood (which they probably define as enough leakage to enter the vault itself) [1].

If you like thinking about seed vault design, then this is a fanciful take on what a seed vault might be like in a distantly-imagined future [2].

Yep. It was easily cleaned up and apparently happens every year in the spring.

but wasn't it designed to be self-sustaining without human input for long stretches of time?

Which it continues to be. Nothing near the vault was threatened. The only thing that flooded was the entrance.