The only reliable way to make backups of versioned ArcSDE geodatabases is through
database tools. Copying the SDE.DEFAULT (or any other) version to file geodatabase
(or any other export format) will not capture any other branch in the version tree.
ArcSDE export format will not capture tables which are edited together (feature
datasets) at the same moment in time, and won't be cognizent of domains or other
geodatabase functionality during restore.
Even with database tools, you must be certain to capture all tables at the same
moment, including the SDE user metadata, and if you intend to repair just one
versioned table with the backup, you need to be prepared for some difficult work.
- V