Does your BaseCamp data have this issue?
You will have this issue if you imported routes containing route avoidances from MapSource into an older version of BaseCamp (before 3.1.1). When you launched BaseCamp 3.1.1, you would have seen the message in the screenshot. After BaseCamp started up, you would have noticed that your data has been cleared.
How to get your data into BaseCamp 3.1.1
1. Uninstall BaseCamp 3.1.1
2. Install BaseCamp 3.0.6 (from here)
3. Launch BaseCamp 3.0.6
4. Select all your routes and click File->Export Selection.
5. In the Save as Type, select "Gps eXchange format" and save to a file.
6. Delete all your routes
7. Delete the folder %appdata%\GARMIN\BaseCamp\Database\3.1 if it exists. Make sure you delete the folder and contents, not just the contents.
8. Install BaseCamp 3.1.1
9. Launch BaseCamp 3.1.1. (BaseCamp should now migrate all your data except your routes)
10. File->Import to get the routes you saved in step4.