QGIS » QGIS Application

For a few years we have had one computer keep a QGIS project and related layer files in a folder on a network directory and we all open that project. After upgrading to QGIS3 someone re-saved many layers as GeoPackages (they were formerly zipped shapefiles). After having the project open for a while (and it is running just fine, by the way) when attempting to close the application, QGIS become non-responsive and it cannot be closed by the task manager (I also tried a couple 3rd party apps such as TaskKiller). The computer must be shut down or restarted. Re-opening the project reveals one (or more) GeoPackage layers are invalid and they cannot be deleted unless another project is loaded into QGIS. Note that all layers in the project are set to read-only and no editing is ever done. Saving is done if styles are changed.
The host computer is Windows10 64bit - satellites are: Another Windows10 64bit, a Windows10 32bit, and a Windows7 (can't remember, I think 32bit.) Note that the Windows7 computer never has this problem and QGIS closes just fine for that machine (so far).