I've checked and the copy+upgrade does transfer the rank correctly. It's possible I already fixed this in v2.6.
Interesting.
The template I noticed that this happened to was originally copied from a 3kt, then I expanded it to 6kt, then later upgraded it from there.
Maybe something about the particular upgrade path caused the issue.
I repro'd it originally (or so I thought), but I did not document the exact steps, and I can't repro it now.
Starting to seem like a run-of-the-mill PEBKAC.
What about formations led by under-ranked commanders not getting replacements?