Yes, that's the way to go. Just check with them what happened, they will be able to see quickly what VAT has been filed and then you can compare with your own data. Maybe, nothing happened in the end. And if, then your company would only have been used as pass-through for the invoicing as otherwise, you would have to pay VAT or get back from the scam, in both cases they money would go into your bank account.
Check VAT statements filed vs. what should have been filed. If you see 1M passing through your company, then you can alert the authorities and tell them where to catch your accountant.