They could and probably would. But since it's two PNRs, the question is more on how long your cnx is. If you're arriving in IST at say 0800 on Day 1 and your next flight leaves at 1700 on Day 2, they probably will not tag your bags all the way. If you're under 24 hours, they might. They certainly would tag if it's a same day cnx.

If it was the same ticket, it would be a different story because they would probably be entered into the system as a connection and would probably do it without any hesitation -- LH and OZ have printed bag tags for me that have spanned over three calendar days over two or three *A carriers on multiple cnxs on the same PNR.