It turns out that there is no way for me to post this issue on Microsoft Connect since Win8.1 is not on the product list. Anyways, a series of questions comes first - anyone has noticed this? Anywhere I can report it (besides here)? Will it be fixed?
Steps to reproduce:
1. Use DISM to integrate all released Windows 8.1 patches, including KB2959977 and KB2980654
2. Boot to Windows (VM), verify that no more available updates in Windows Update
3. Call DISM /ResetBase /StartComponentCleanup against the image on the VHDX
4. Boot to Windows (VM) again
Result: now Windows Updates require you to install KB2959977 and KB2980654 again.
Cheers
Chris