Update as soon as possible to avoid this issue.
DS SOLIDWORKS Corporation has detected a workflow that may result in the FeatureManager missing items or having entities listed at an incorrect position in the FeatureManager. This issue may occur with files that have multiple configurations during the conversion of data from a prevision version to SOLIDWORKS 2012 SP0 or SP1. Files created in SOLIDWORKS 2012 are unaffected.
SOLIDWORKS 2012 users are strongly encouraged to upgrade to SOLIDWORKS 2012 SP2 as soon as possible to avoid this issue. A hotfix is also available for SOLIDWORKS 2012 SP1 users and attached to Solution S-058181.
Symptoms: Affected files will be missing entities in the feature tree, such as features and mates in one or more configuration of the model.
Correction: The fix in SOLIDWORKS 2012 SP2 and the SP1 hotfix prevents the issue during conversion. In many cases, the fix can also repair affected files that have already been converted. Once repaired, the issue can not recur.
If SP2.0 or the SP1.0 Hotfix does not resolve the issue with a particular file set, then please collect the problematic SOLIDWORKS files and contact your SOLIDWORKS Reseller for further review.