In version 21.1 I have noticed the following behavior.
If I update my Visual Studio traditional app using a new version, and then open the existing AIP file (it will detect the new version and notify me of that), and then immediately ask to build the MSIX package, it will now fail claiming an issue that the aip file cannot be found.
Normally, I believe the build request would save off an updated AIP file with the new version and then build it. I suspect an issue with the file being locked.
If I open the API and then save it, I can then build the MSIX package without issue.