Maybe I should recap the chain of events re-reading myself I'm probalby a little hard to follow.
Hmm. You made setup changes while a recording was happening. While what you observed probably shouldn't have happened, I suggest that you ignore that case and test again when you aren't making such significant changes. Small changes like tagging and so forth would be fine, as long as you aren't tagging the file that is still being recorded. But connecting a new Cleint to the Server, and changing the Access Key, is kind of major.
I also often get stuck with a bunch of Time-shifting folders that don't get deleted on the server (not sure if it's related though probably not to this issue)...Might be due to the crash on the client machine last night? (I forgot to mention the client machine also crashed a little after...)
I would put that down to the crash. There used to be a bit of a problem with left over Time Shifting files, but that has been mostly addressed. I believe there are still some circumstances where it can happen. I watch live TV from my client occasionally and I did get some left over files the other day, but I was mucking around a lot, and may have even killed the client in process. At least the client Time Shifting files are now clearly named, so you know what they are.
Clean up any left overs you have now, and if you see any more, document exactly what you did and report it. If you can reliably reproduce the issue in a repeatable manner, Yaobing would like to hear about it.