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The problem is, with what media would you replace them with if you had to replace them somewhere between then and now? iomega zip drives? Jaz drives? CF cards? sony memory sticks? rewritable cds/dvds? Imation superdisks?

They could've replaced floppies multiple times, with all the certifications and hardware replacements and new procedures and regulations, and we'd still be using (a different, but still) "obsolete" medium for this now.

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Agree. For a purpose-built system that is only used by trained professionals, being "up to date" really means nothing. There's only fitness for purpose.

But the cost of switching -- mainly thoroughly certifying the replacement system, retraining, and the risks of an error happening during one of those processes causing a catastrophe -- that's real.

There's no point in upgrading the storage mechanisms of arbitrary systems, or completely redoing the whole system from scratch on new hardware which would be the case here, unless it yields measurable improvements in fitness for purpose to balance against the switching costs.

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