O.K., I got myself into a bit of a mess here. I'm pretty sure I know what happened but that doesn't help me get out of the situation. But before I ask about my main problem I would like to ask another question first.
I have installed and purchased PM+ as an upgrade to PM6. So now I have a working copy of both PM6 and PM+. By design, if I update the metadata (or move) a catalogued image using PM+ then the catalogue is updated appropriately. But if I inadvertently use PM6 to make the changes, then I assume that the catalog is not updated. Is this correct? Is my best course of action to remove PM6 from my machine since it is no longer providing me with any additional capabilities?
On to my current problem. Here's what I have been doing. I ingest my raw files (raw only). I cull, rename and add metadata. I add them to my working catalogue. I then select those photos that I wish to further process and copy these to a separate folder. I then use my raw editor to process these photos and produce jpegs. I then copy both the raw file and the jpegs back to my original folder (with the copy set to overwrite). The reason I copy the raw file back is because I want my edits (filebase.org.pp3 files) copied as well and I don't think that would occur if I just copied the jpegs. Anyway it seems that my "bombing" of my catalogued raw files is causing issues. If I browse by capture date (my file structure is based on capture date) in the organizer tab, everything looks fine. However, if I now right click on one of the raw files that I have bombed and select "open in context", I get a navigator window of the appropriate directory, but that raw file is now shown as not being included in the catalog.
So I guess my question is, how do I bring everything back into sync?
However, as I type this question out, it occurs to me that while the "navigator window" view of the status of that file is wrong, it probably doesn't matter with anything that I would want to do to that file going forward.