That problem occurs because the files you are checking in are not within the range of folders your Inventor Project file can see.
Generally (for Vault projects) you place your Project file in say "C:\VaultWorkspace" and then configure the Workspace setting in the Project to point to say "C:\VaultWorkspace\Designs" - this is a "relative" workspace (because it's a sub folder of VaultWorkspace). Relative workspaces are a basic requirement of Vault projects.
If you had the above setup, and then tried checking in a file that was not in C:\VaultWorkspace\Designs (or one of its sub-folders) you would get the error in the screen shot you have shown.
So do I have to have the Vault project point to a subfolder on C, rather than the root directory?
Right now I will have several folder in the root directory that will need to go into Vault. Should I set the it up with C:\Customer1 workspace, and then change the workspace to C:\ Customer2 when I go to load the Customer2 files? And should I move the project file itself to those subdirectories as I am loading them?
I guess that is what I was trying to avoid because I'm only vaguely familiar with all of the pointing workspaces and projects where they are supposed to go.
Vault is brilliant - but it does need to be set up correctly. Not understanding Projects, Workspaces, and how Inventor works with files is going to get you into a very deep hole very quickly. Vault is not the kind of tool you can just install and run unless you did lots of homework beforehand and had that underlying file-structure knowledge.
I can't talk you through the setup step-by-step here on the DG. Suggest you talk to your VAR and get some help. It might cost you, but whatever the cost, it'll be a lot cheaper than the hours you'll spend getting it wrong and getting frustrated. Step one of the learning process - read up on Project files and how they work.
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