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

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.

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].

Water entered the vault tunnel but did not reach the seeds. Nonetheless, your point stands.

This was the first thing I thought of too!