I have discovered a workaround which is working fine (... for me with two mouseclicks):
Immediately after the SEP Processing I run a predefined export to replace the SEP-TIFF with an exported duplicate TIFF. After that it is possible to write LR changes to the file with no problems.
This workaround didn't work for me under XP and it still doesn't work now that I am running Windows 7 64-bit + LR 64-bit. However, I have no problem if I first create the TIFF file via the Export command and then "Edit [original] in..." SEP 2 afterwards, which is even faster.
This solution WORKS 100% for me.
Are you aware that the problem has been fixed in the latest release of the Nik Software plugins? There's no longer any need for a workaround. Just install the latest versions.
For those who still have this problem in LR3 or LR4 for images processed before Nik Software updated their plugins, here is a solution that worked for all the TIFF/JPEG images in my Lightroom library that where hit by this issue:
1. In Lightroom right-click the image and Edit original in Photoshop.
2. Do some change to the image and undo it immediately (this is just to enable the Save menu). Hit Ctrl-S .
3. The saved image is reloaded in Lightroom.
4. Click on the upper right icon indicating that the metadata and the Lightroom catalog are no longer in sync and retry writing the metadata to the file.
5. Problem gone.
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