I use LOR S3. The "best practice" methods when changing from 2011 to 2012 is to either:
1. Add any new channels to the bottom and only to the bottom of Track 1 (the "Master Track"). Once there, copy them to Track 2, Track 3, Track 4, etc... and then you can move, rename, delete all you want. If you never move or delete channels in the Master Track, it is very stable when creating new sequences and applying saved Channel Templates. If you start moving and deleting in the Master Track, it can get crazy.
2. Create a whole new channel layout from scratch. Call it 2012 Layout. Then open the 2011 Sequence and copy/paste into the new sequence. If you use choice #1 for a year or two, you will eventually have to use #2 just to make sense of the new changes.