When you copy files from DVR to imports you might often see duplacate listing. One listing pointing to files that no longer exist. Channels should clear this up on its own, in time. I usually do a manual "purge deleted"
As far as meta data / matching goes. When you manually edit metadata in channels that data is saved in channels not appended to the actual files (i think). There are programs you can use to manually edit metadata on file itself. Note: I rename all my imports with filebot. I have been happy with the results.
When matching shows channels uses Gracenotes. From what I understand Zap2it uses Gracenotes too. So you can search for series id on there. If Gracenotes does not have it in there database, only thing you can dobis manually edit the metadata.
Also what show was it