Templates ntf new ODS

I have converted all dbs on my server to 8.5.1 ODS by shutting down the server and ran ncompact -c.However, I can see templates did not get the new ODS. Is that normal and why?

Also, is there a way to run ncompact -c only on the domino data? Have you guys tried “ncompact -c sys.ind” where sys.ind content would be ""

Basically I don’t want the data sub folders to be affected

Thanks in advanced