All editions of Microsoft Word from time to time suffer from bug in numbering. Instead of a number, black box is displayed. Sometimes it happens right after document is opened, sometimes during editing. Probably some internal structure of document gets corrupted, so based on level of corruption, different fixes could help. Many of them are listed at https://answers.microsoft.com/en-us/office/forum/office_2010-word/ms-word-header-styles-are-showing-black-boxes/c427b21c-dcda-46ce-a506-b9a16c9f2f3f
I took different approach. Since docx is just standard zip package with xml files, I decided to try if I can fix it manually. And it worked.
When I extracted the docx, there was file called numbering.xml in word folder. When I examined that file, I found strange section in heading that was causing problems. This w:rPr tag wasn't present on any other of level definitions.
When I deleted that tag and re-packaged the docx file, all worked fine.
Now back to productive work, fingers crosses that the document will stay as is for now.