Thanks for posting the requested log. Here is what we know about the issue which may help you resolve this for yourself until this is officially fixed:
packages for assets are not being found when upgrading the project because they are looking in the new folder (with the version appended) and the Paths list that has the old folder in it.
Ultimately it arrives at PackageTools::IsPackagePathExternal where it checks if the path is a part of the project. A final list of packages that are external are gathered and reported.
The old folder comes from the Saved/Config/Windows/Engine.ini that was copied along other content from project-to-convert. The ini contains paths for the old location. If you suppress copying of this folder everything seems to work fine as Saved/Config ini’s are rebuilt by the UE4.
I have not tested this, but you might try to, with the Engine closed, remove and save to a safe place the “Saved” folder then reopen the project and let UE4 rebuild this directory. However, there may be data there that the engine is referencing that will not automatically update. In which case, you could try troubleshooting by systematically replacing individual ini files in the original “Saved” folder from the newly generated “Saved” folder (starting with Engine ini) opening the project after each individual replacement.
These suggestions are not proven to resolve the issue but something relatively easy to try in the meantime until the reported issue is officially resolved.