Have you run the Validate Shortcuts command? Rt click on the shortcuts folder to access the command. If it finds invalid shortcuts it will prompt you to fix them or delete them. Assuming you still have the source objects in a dwg, you can browse to those files and pick the object that applies. That is one option.
Another option is to use the shortcuts editor (found in the Autocad folder on the start menu) and re-path the shortcuts to the proper files/objects.
Update: FYI, shortcut links can be based the source object ID or Name or both. By default the link is both. Thus if the source object gets recreated or renamed, the link can be re-established. For example, if a shortcut is linked to a surface model called EG in a dwg, and a user deletes the EG surface and creates a new one with the same name, it will have a new object ID, but the same name. Thus any shortcuts to that surface will remain intact because it has the same name as before even though the ID has changed. So part of your solution is to re-store any objects that got erased or changed by restoring the name to what it was in the shortcut.
Again, this can all be fixed with the shortcuts editor.
Neil Wilson (a.k.a. neilw)
AEC Collection/C3D 2024, LDT 2004, Power Civil v8i SS1
WIN 10 64 PRO
http://www.sec-landmgt.com