I in a way understand what you say and puzzled that I am the only one that seems to have this problem with Nikon NEF files touched by CNX2.
Perhaps most people decide on the orientation they want for their photo while they are editing in CNX2 and don't try to further rotate the photo after this editing has been done. BTW those NEF file aren't just "touched" by CNX2. It writes an entirely new NEF with slightly different structure.
Do I understand it correct that I can keep using CNX2 for NEF files created by supported cameras, for both already edited NEF files and files to be edited for the the first time?
Or should I use for CNX2 supported NEF files to be edited the first time ACR, as I have to do with files of the new Z-Line cameras (not supported by CNX2) anyhow?
And this also brings up the question how to set the IPTC/XMP preferences in Photomechanic Plus:
Do I use the provided Snapshot for "ADOBE Products" or the Snapshot for "Nikon Capture NX/NX2" or even a MIX of both?
This gets a bit complicated...
The obvious problem with mixing CNX2 and Adobe (ACR or LR) are that they handle XMP differently. CNX2 expects the XMP to be embedded and ignores any XMP sidecar. ACR/LR (and other Adobe products) will not embed or modify embedded XMP and always update the XMP sidecar. However, if you have both embedded XMP and an XMP sidecar, then ACR uses the XMP from the file (e.g. NEF or XMP sidecar) with the most recent date. Most cameras these days at least write some tiny amount of XMP in order to store the rating.
If you only use ACR/LR then the RAW NEF file remains untouched (and modification time remains as is) - all XMP is put into the sidecar. You can set PM to do the same by unchecking the "Allow RAW files to be modified" box. This is how we recommend the settings when working with ACR/LR only, and in general it is recommended that you leave the RAW files unmodified and only use XMP sidecars (it is the safest thing to do).
Unfortunately if you open that NEF in CNX2, it will not see that XMP in the sidecar and it will ignore it. So then if you save the NEF out from CNX2 (with same name), guess what happens if you go back to ACR/LR (or even PM)? I believe ACR/LR will use the stale XMP that was originally embedded in the NEF because it now has a more recent date (this is how PM works). So you will essentially lose the XMP that is in the sidecar and any further edits in PM will overwrite a new XMP sidecar. Same problem if you write a new NEF (Save As) from CNX2 - the embedded XMP won't have any of the XMP that was in the sidecar.
If you edit in CNX2 first then any XMP you might add will be embedded. If you then do additional editing in ACR/LR (for some reason), it will read the embedded XMP just fine. But if you make adjustments in ACR, then all embedded XMP will be written to a new XMP sidecar along with ACR's adjustments.
Since you are working with CNX2, you need to have PM embed XMP into the NEF so CNX2 can read it and preserve it when a new NEF is saved from CNX2. So you need to make sure you check the box to "Allow RAW files to be modified" and also check the box to "Add embedded metadata" (I write both XMP and IPTC but XMP only should be fine).
For the "Always create and/or update XMP sidecar file" box, if this is not checked then PM won't create an XMP sidecar if it doesn't already exist. But if an XMP sidecar does exist PM will always update it to keep it in sync with embedded the XMP. So if you uncheck this box and only use PM & CNX2, you should never see an XMP sidecar.
But once that NEF file is "touched" by ACR/LR you will now have an XMP sidecar that CNX2 will ignore. Therefore, any ACR adjustments will only get added to the XMP sidecar (once the NEF is opened in Photoshop you can't add IPTC type metadata to the NEF file).
If you use Lightroom this gets more complicated because it can add IPTC type metadata to RAW files, but again it doesn't modify the actual RAW file (e.g. NEF), it only updates the XMP sidecar. Therefore if you add a bunch of metadata (e.g. keywords) in LR and you want this metadata to flow into CNX2, then you need to touch the file in PM (e.g. tag/untag) or use the "Update IPTC/XMP" tool (ignore the option about JPEG/RAW). PM will read the XMP sidecar which has the most recent metadata, and it will update the embedded XMP to match the sidecar. Then this will flow into CNX2.
HTH!
--dennis