I don't have more context than what's in the article but what it sounds like is they've lost access to the database that says $2000 from this pile of $10MM belong to John Doe, because the company that hired the devs who understood this stuff is bankrupt, and the involved parties can't seem to reach an arrangement to bring in a cleanup crew. I don't think any money is actually missing.

Ultimately a modern bank is just a software system pushing around the proverbial proto between some databases and other financial software systems.

Yes but some of those databases are highly regulated and some are not, and the distinction between those (and in some cases deceptive advertising around it) is the crux of the issue here

I’m willing to wager that there is money actually missing.