By default bolted connections save in sub-folder of a folder named by the assembly they are inserted in and they have a super generic file name. This causes issues because you can easily get 20 folders for bolted connections only and multiple bolted connections with the same filename. Multiple bolted connections with the same file name can cause havoc if you ever have to relink them.
My suggestion is to have an option to save all bolted connections in a single folder in the root of the project folder. Also each bolted connection file would have a unique file names based off of the project name.
Some co-workers and myself are doing this manually but it's extra work and some times it gets skipped. Having this would save time and trouble.
Here is a thread which discusses the same problem.
http://forums.autodesk.com/t5/Inventor-General/bolted-connection-naming-problem/td-p/3847957