I just rebuilt my development machine. Fresh windows install, fresh install of Unreal and visual studio. Im now getting the exact same issue when creating a fresh 5.5.4 project.
I create the project. Everything works great. I close the project and reopen it.. i get the message
The following modules are missing or build with a different engine version
MyProject
Would you like to rebuild now?
if i click yes.. it fails..
if i try to open the project agian, everything works fine.
This feels like a bug.