Problems syncing and saving metadata

Question

I realized the time on my D40 had crept 72 minutes off from what's right, so I wanted to go back and adjust the time in the NEF files. Early on with Lightroom, I learned not to do this inside Lightroom (posts like: http://www.adobeforums.com/webx?224@@[email protected]/7), so I used exiftool. (Is this still true in Lightroom 1.3.1, or is "Edit Capture Time" safe to use now?)
Adjusting the dates inside the NEF files using exiftool works great, but now I have to get Lightroom to notice the changed dates. I hoped "Library->Synchronize Folder" with the "Scan for metadata updates" would do this, but it seems to have no effect. (Should or shouldn't it?)
If I do "Metadata->Read Metadata From File", it does notice the new dates, but also (after warning me) loses all the metadata and develop settings I've applied inside Lr. The develop settings reset actually shows up in the history, and it's easy to go back to the prior ones, but I have to do this for each photo. It seems the Synchronize feature would be a better way, if it worked.
I also still have problems with Lr refusing to actually create XMP sidecars for many of my files, even when I explicitly tell it "Metadata->Save Metadata To File". As far as I can tell, Lr doesn't actually write XMP when you do Save Metadata unless it thinks something's changed. Problem is, it doesn't always know when something's changed. A trivial example is: tell it to write the XMP data, then go delete the .xmp file, then go back to Lightroom and tell it to write the XMP file again; it won't. A less trivial example is what actually got my files into this state -- I copied the NEF files onto both my laptop and desktop computers, then added them to the Lightroom library on the laptop, did some stuff including writing the XMP files, exported a catalog with the new photos, and imported this catalog on the desktop. Now Lr on the desktop seems to think the XMP files exist there, even though they don't.
The reason I'm complaining about this in the same context as inability to sync metadata changes is it prevents me from doing a manual sync with no data loss: if Save Metadata always worked, then I could invoke that (putting Lr's current metadata in the XMP files), then tell exiftool to operate on both the NEF and XMP files, then tell Lr to read metadata, and a lot less metadata would be lost. But I can't convince it to write the XMP files in the first place.

Answer 1

Also, for a test image where I checked whether Lr still has the easy-to-demonstrate form of the won't-write-XMP problem, and I told it to write the XMP file, then deleted the XMP file from the Finder, then went back to LR, it's doing something new -- the metadata panel shows "sidecar files: .xmp", but the thumbnail in grid view has a question mark badge in the upper right which I don't remember seeing before. If I hover over the question mark, I get a tooltip which says "Sidecar file missing."
And still, if I tell Lr "Save metadata to file", it doesn't recreate the XMP file. Or complain more vociferously about the file which it knows is missing. Weird, huh?
If I click on that question mark icon, I get a dialog that says: "The following files (related to this photo) were present before, but are now missing", with the name of the .xmp file, and "The photo negative file is still present. Do you want to forget about the sidecar files, or continue to track them? [Continue to track] [Forget]".
If I choose "Continue to track", things stay exactly as they are (no .xmp file, but the question mark badge remains). If I choose "Forget", the question mark badge goes away, and "Sidecar files: .xmp" disappears from the metadata panel. But there's still no .xmp file, and the "Save metadata to file" command still doesn't create one.
Anybody know how I can force Lr to think it's worth its time to write the .xmp file?