Hi ACH,
The .metadata folder is where your CrossCore Embedded Studio (CCES) preferences and intermediate files created by Eclipse plugins, for example, are stored. The .metadata folder your CCES workspace.
A workspace isn't necessarily required to ensure that your projects can be used; any projects that you have created (and added to source control) can be added to a new workspace using File | Import.
You can also use CCES headless tools to automate building of your projects - FAQ: Using Blackfin and SHARC from the command line in CrossCore Embedded Studio.
The main item that I think you'd want to keep with your CrossCore project is their launch configuration settings. Those can be transferred from your CCES workspace (.metadata folder) to your project folder by choosing Common | Shared file in your launch configuration(s) and selecting the CrossCore project.
If there are any other preferences, for example, that you're specifically interested in backing up or storing with your CrossCore project(s), then let us know.
Hope this information is useful.