Of course it's allowed. It would be under one of the Merchant Error chargeback codes since the intent was never there to tip $1000 (and it happened due to an error in their software).

If it's not classed under that code there's also 'Friendly Fraud' code for misrepresentation.

It’s allowed once, at the very least, if the merchant is hostile or unreachable.

Most credit card companies it would be no problem at all. It shouldn’t be necessary though, a quick call to the merchant should be all that is necessary for them to void it.