Istanbul to Mumbai on a single ticket

I have a ticket from Istanbul to Mumbai with a stop at Abu Dabhi. The IST-AUH section is on the Turkish airlines and the AUH-BOM is on the Etihad airlines. The whole ticket is in a single PNR but the Turk gave me his own PNR and Etihad gave me his. Both PNRs list the entire trip. Since these two airlines are not part of the same alliance, will my bags go to Mumbai? The scale in AUH is 2 h 20 min and if I have to re-register my bags for Etihad, I doubt that this scale is sufficient.