Thanks for the files, and sorry for the long delay. We've had hurricane Fiona and a number of other things going on.
In 4.1.10 the UI no longer remembers the JSON export version from the last export. This prevents the version from getting set once and then never updating to the latest version. Users should not be using this setting very often, so needing to set it manually should be acceptable. Note the version is still set from an export settings file when choosing such a file or when doing a CLI export, just it is not set in the UI when loading the last used export settings.
You mentioned one project file should use an atlas scale of 0.2 and the other 1.0. I assume you meant the texture packer settings when doing JSON export? We looked in both project files and the texture packer scale for both was stored as 0.2. From what we can tell, it is working correctly and loading the values stored in the project files.
It may be there is a bug that caused the wrong scale value to be saved in your project. If you do an export with 1.0 then save the project, it will store that scale in the project. If you can then find a way that the scale gets set to 0.2 when it should not, then we would be very happy to fix it!
