Hi everyone,
I had a similar issue with a set of deleted iCal calendars. In my case these were calendars from an iCal Server I no longer use (I stopped using the iCal Server in the first placce,because MobileMe automatically syncs all calendars, but my iCal server was only allowed to have a local IP and hence was not reachabe from home or the iPhone...)
I deleted the server entry in iCal and the calendars were invisible. They were not synced via MobileMe anymore. But they still DID show up in iTunes when syncing my iPhone, which I do sync via iTunes, as I have another calendar I share between work and home but do not want to have on my iPhone (thanks Apple for not letting me choose which calendars and address book groups I want to share via MobileMe, let alone on a per-machine basis).
Anyway, I have now done the following, probably very dangerous(!) thing:
In the finder, I went to User > (MyUserName) > Library > Application Support and put the folder "SyncServices" into the trash. I did not empty the trash, so I had some sort of backup in case horrible things were about to happen... For good measure, I restarted my Mac. After coming back up, I opened iTunes: ALL calendars and address book groups were gone from iTunes. They still showed up in the respective programs, though, thank god! I then force-synced MobileMe, using the "replace data on this computer" option which resulted in a rebuilt "SyncServices" folder. Since then, the deleted calendars are gone from iTunes, but the other ones show up in iTunes again and are syncable to the iPhone. I can not recommend this to anyone, because a) I do have a MobileMe account to sync to/from and b) I am not a all shure what it was that I did there and what the consequences might have been. All I can say is: it worked for me...
Best
co-operate