The Current File Is Not The Latest Version

When working in Inventor and switching between multiple files within the same assembly you can in one particular scenario, encounter a message such as:

• A later version of this file has been saved by <username>. Saving the file would overwrite changes, which is not allowed. If you wish to preserve your changes, use the Save Copy As command.

This message appears because at some stage you performed an Open From Vault and chose to overwrite the local files when this message appeared:

• File 'path\filename' is checked out to you. Are you sure you want to overwrite it with data from the Vault?

You can avoid this by changing the response from the Default Yes to No.
This is an extract from the Cracking the Vault, Manufacturing Community Blog