You can ask the check-in agent at ASR/NAV if the bags can be checked all the way to ATH on the separate ticket. Most likely the agent will be able to do it. If not, it is not the end of the world as you have plenty of time to collect the bags at IST and proceed to the check-in counters upstairs; not a big deal.

2½ hours for this is more than sufficient even when on separate tickets.