Had a single ticket issued by KLM from Prague to Moscow via Amsterdam. I have SkyTeam Elite Plus status. Flight from Prague has been codeshare with CSA but operated by Smartwings. Much to my surprise, CSA rejected to check my luggage through to the final destination, saying that they do not have the respective arrangement with KLM. Both companies are SkyTeam members and my flight has been presented as KLM flight. Consequently, I have been forced to pick up my luggage in Amsterdam, leave the terminal, check-in again, pass security and passport control. Rather than having my planned meeting in Amsterdam, I had to deal with my luggage. I was checking with KLM and they confirmed, that there is indeed no agreement between these two companies and CSA is right. And it is despite the fact, that flight has been marketed and sold as KLM flight. Another problem is, that you purchase a ticket with 4-star airlines to end up with poor quality 2-star low-cost, which does not even let you choose your seat for free (despite my Elite Plus status). Therefore, be aware of the codeshare. You might be paying for one service and get something very different.
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