So it seems like Slack took them off the nonprofit plan. That's a different story altogether and makes more sense for the timeline involved.

If they determined that Hacker Club violated some terms of the nonprofit demanding they move to regular or be kicked out seems not as bad

I can't imagine any scenario that justifies an out-of-the blue demand of $50k within a week or your data is deleted. The only way this isn't an awful thing to inflict on a teen education nonprofit is if there have been conversations happening that weren't disclosed in the post - conversations that would have illuminated this possibility.

Not saying this is the case, or that slack thinks it is, but -

If slack found out that the company isn't really a non-profit, or that it violated the requirements in the non-profit agreement (such as promoting discrimination) it would justify a demand for immediate payment in my opinion.

The article says slack took them off the non profit plan, set the price at $5000/year and they paid it and were happy to. It's not a long article.