In Hyperledger Fabric v0.6, a supply chain app can be implemented that allows tracing of provenance and avoids double-spending (i.e., distributing/selling items more than it has
At the moment there is no straight forward way of providing provenance across two different channels within Hyperledger Fabric 1.0. There few directions to support such scenarios:
First one is to have an ability to keep portions of the data of the ledger and provide discrete segregation within the channel, the work item described here: FAB-1151.
Additionally there is proposal of adding support for private data while maintaining the ability to proof existence and ownership of claimed asset was posted in mailing list.
What you can do currently is to leverage application side encryption to provide privacy and keep all related transactions on the same channel, e.g. same ledger (pretty much similar to approach you had back in v0.6).