[BScout]

Originally Posted by dg27

Not sure what you mean be a "default workspace". Do you mean the session I'm working on?

Pro Tools menus>Window>New Workspace>Default Workspace
click on your session in the left column
click on the "rendered files" to see all the rendered freeze files and manage them

To be clear, if there are missing/offline files in the workspace from linking, you will always get error messages when opening Pro Tools sessions.
This is the area you should be managing your audio files that are in use.

Originally Posted by dg27

Also not clear what you mean by saving a "version up."

Save your Pro Tools session with a new version number.
If you don't already do this, you should learn to in order to prevent loss. That way you have previous sessions before you clear clips/renders/files that you can revert to in case something goes wrong. (of course, this will not restore deleted/trashed clips)