This has been a major pet peeve since my boss got the Microsoft Surface – deleting the ink comments is often a pain.
The simple approach is:
Under File Menu, click on Check for Issues. The button expands to give multiple options. Click on Inspect Document.
The “Document Inspector” window will pop up with a long list of options, all selected. Just click on okay.
The first diagnostic message will mention that Ink Annotations were found. Click on the Remove All button next to it.
The window will show that the same has been done. Now just click close and then save the document. Voila.