Erik bunq won't send notifications for old transactions and no actual transaction data has been affected in the first place. The third-party app can and should always get all past transactions that weren't synced properly by calling the respective API endpoints themselves. If they don't do that, then you would probably have to do it manually or by importing an account statement if that's supported by your app.
Relying solely on the callbacks/webhooks (what broke last weekend) isn't a great idea. Not sure if anybody does that, but if your third-party app seems to be doing this, the quality for their bunq integration should be called into question. After all, even if rare, outages can always happen. Not just at bunq, but also for the third-party app itself. The callbacks are "nice to have", but they're just one part of an integration. If that's all an app uses, they're asking for trouble. Most banks don't even offer them.