Why has my CIS deduction on original invoice now disappeared after printing and sending to customer?

There is an on-going investigation, info.

Some users, like you, are experiencing this kind of issue. For now, our engineers are working diligently to get a permanent fix.

While they're still working on it, I suggest reaching out to our customer care support so you'll get added to the list of affected users. Here's how:

1. Click Help inside QuickBooks Online.
2. Select Contact us.
3. Enter a brief detail about your concern, then click Let's talk.
4. Click Start messaging.

The chat line will be open from Mondays to Fridays from 8:00 am to 8:00 pm BST. 

If you have other concerns, please don't hesitate to pop a comment below.