I will do my best to explain what is happening.
The library showing issues is the one "owned" by work. It was created in fusion, in a team that we all access, and it lives in a project inside that team. The team is owned by the account of one person in our company, and the rest of us are added to the projects in that team. We have all had access to the project that owns the library and have had that access for years. We also store all the 3d packages in the same project in a folder dedicated to them.
I have my own personal library that was created inside the team associated with my account. NOT the single user workspace, it's the main team for my fusion account. It also lives in a project folder, with a folder for 3d packages.
The parts we're having issues with are parts that I had created inside my personal electronics library, and then we decided we wanted to use those same parts in the company library as well. In this case they were some connectors, and an ESD Diode. We already had a schematic that would work, and a component that they'd fit in, so from our company library I clicked add footprint, import, selected my personal library from the window that came up, and selected the footprint I wanted. As far as I could tell that copied the footprint and 3d package into our company library. I could open and edit the package, it would populate onto PCB 3d files, it worked as I would expect.
This past week we made a new board, and used these connectors on them. This board was created after the latest update. The files were in a project/folder that all of us have had access to for years, but it is a different project from where the library is stored. When the 3d file was generated the models for these connectors did not populate, it just gave the default flat rectangles. If I clicked on the footprint in the layout and selected package, I could see the preview of the 3d file, and it was active, but it wouldn't populate in the 3d file. That is when we tried editing the 3d package in the library and got the error message posted in this thread.
What I did notice, I could not physically located the 3d package file inside our team. Meaning I went to the top level of the team in the data panel, and did a search for the name of the package file, and it finds nothing. I've done this for all the parts I know were imported from my personal library, they aren't in the team. I had assumed that a copy of the file would be made in our team, but all I can guess is that fusion is actually just generating a link to the file in my personal team, or maybe this is where the library.io stuff is coming into play. (I don't fully understand the role of library.io, I just know we went out of our way to unlink our library from library.io years ago when it was causing problems).
As of right now, the only way to fix this problem has been to upload the step files for these parts directly into our company Team, then for each footprint that was imported, generate a new 3d package, insert the step file, save the 3d package. Then from the component level, replace the package with the new one, and then finally delete the "imported" one.
I only see Team URNs for parts in the company library
The URN for one of the packages that was imported, but now has this issue: urn:adsk.wipprod:fs.file:vf.zH1hJJEXQxOjUB1sKwqs1w?version=2
And the URN for a part that was created in our library originally and doesn't have the issue: urn:adsk.wipprod:fs.file:vf.t8Q_enydRgCF1730mlPDhg?version=3
I did go and inspect my personal library, because I have parts in there that were imported from the company one as well. I notice the same thing where the 3d package file physically isn't in my team, but I do not. However the difference appears to be that my personal library does have a link to library.io. Most packages have both a team and library.io URN. Again, I have never actively used library.io, so I don't know what implications there are that this library has a link. If I try to edit one of these imported packages I get the message "This package isn't found in the current Team Hub but exists in library.io. Would you like to import it into the current Team Hub for editing? The imported package will remain linked with library.io.", however if I say yes, import, it throws an error "failed to retrieve 3D package info. Content access denied error".
So it looks like I'm seeing issues in both places.
