When saving a Microsoft Word document that contains Acrolinx flags, the flags disappear from the document after save task has completed.
Acrolinx flags are not saved within the document nor in the auto-recovery copy of the document. They are removed when an autosave is triggered or when users manually save the document.
Resolving the Problem
For related information, see the FAQ: Acrolinx flags periodically disappear and reappear in Microsoft Word