YMMV, but I did something similar last year. I purchased one of the last Rimowa bags with the e-tag at Lufthansa World Shop in FRA. I did not have any issues at all checking the "2nd" bag in at the counter, even though I had one bag checked already from my first intra Europe leg of my ticket. First leg was on LH, second was UA to SFO.


I will say, I wouldn't recommend checking an empty bag, as the likelihood it could get damaged would be something I'd worry about. In my case I had planned to purchase the bag ahead of time. I had an old bag that I stuffed with clothes on my first leg as a carry on. I then transferred (entirely) inside the new bag, so as to give it some support and avoid the new bag being crushed or damaged if empty.