Your rename issues may not be related to Windchill. We had numerous issues in regards to renaming parts in SW 2010. All of the issues appear to be resolved with SW 2012.
You may want to test renaming the same assembly with and without Windchill.
My first question would be - Does Windchill handle SolidWorks file referencing the way other vault do? EPDM allows renames within the vault and will update assembly paths correctly when it's checked back in. Does Windchill have the same functionality? If not, then you're back to renaming files as if they were on a network drive and using SolidWorks Explorer for instance.
If Windchill does handle the references, then you're better off checking with the Windchill admin and their forums.
Windchill handles it pretty much the same way as other vaults. All paths and references should be updated when it gets checked back in. I've posted this on PTC's site, as well as escalated the issue with our IT group. Unfortunately, it sounds as though our case is pretty rare, as most companies with CAD stick with native PDM solutions. Windchill has been great for us up until this issue. Since we run both Solidworks and Pro/E, we needed one PDM solution that could handle both.
@Mark - thanks for the reply. We've "pack and go"-ed the assembly for export out of Windchill and will be testing the renaming functionality outside of the Windhill environment. Luckily we are migrating to Windchill 10.1 soon along with upgrading to SW2013. It's a bit of a balancing act, as we run multiple versions of each software depending on our clients needs.