its a strange behavior
after closing your project, open the .prj file with a notepad editor and check if the libraries are present in that?
also make sure if you have the write access to the .prj file
The prj file looks good, this whole project seems cursed. It originally started in Orcad, then converted to an earlier version of DxD, then had the dproj file converted to prj to bring us to where we are now. I have library issues, non-common properties and parts that won't verify.
What a mess.
there will be issues always in the schematic which are converted to another software,
may be you can take the help of local mentor support team to clear all your queries.