Deleting an item on QUOTE screen does the following:
Deletes the item
Moves the Quote to INVOICE screen
Saves the invoice even if you just use the X Close button.

To replicate this:
I am using the multi-tab layout.
Create a new quote with multiple items.
Save, review that all is correct.

Open the item screen, select an item and use the Delete Selected Item button. Clicking this button does the following:
Moves from Quote Screen to Invoice Screen
Give you the Message Item(s) Deleted.

It has already copied the quote to the invoice screen and saved it even if I select X Close button.

I have a test install and a production install that this is happening on. It is really messing up my invoices.

Please let me know if you can replicate this issue.
Thanks!
Beth