When you get a message like this, it means that ARCHICAD found corrupted elements. These are usually too small to be visible, or has other geometry related corruption. These deletions happen to prevent a Send & Receive issue next time you hit the button.
In almost all cases, it is not visible later that ARCHICAD deleted anything from the project.
On the other hand, I understand why it scared you. I will report your feedback to the responsible people. Thank you.
Customer Engagement Expert, Community Admin