Hi Benjamin,
Sorry to hear this was so frustrating, but it seems you got a happy result in the end. It has been a year since I did this for our systems, so I'm working on old memories now. I seem to recall that in my case, JSPM reported that the SCs were locally modified, but as the system was then no longer under NWDI control it then allowed me to deploy the standard SCs over the top. I did not have to use SDM in this case. Possibly this had to do with it being on NW 7.01 instead of 7.00, although I couldn't swear to that. Also, it may have been due to the fact that I was loading newer versions of the SCs, not trying to load the same version that was already installed. Perhaps that was the source of your issue, though I think "God mode" should then have allowed it anyway.
The real test, now that you've deployed via SDM, is whether it works the way you want it to with your next JSPM deployment. It seems like it should.
As for the 5 hour wait while NWDI synchronized a track with an RTS in which the same versions were already deployed, yeah, that's one of the things I have always disliked about NWDI. It is an exercise in frustration and patience, for sure. I'm not surprised you had to do that. Newer patch levels of NWDI improved this behavior -- it got better at detecting that the same component versions were already in the RTS and so wouldn't always redeploy -- but it still seems to take a long time. I look forward to converting ESS/MSS to Webdynpro ABAP so that the development is in the backend and NWDI is out of the picture. That will be a bit of a project, however.
Regards,
Matt