In case any one has the similar query-
On bound journey Lufthansa (LAX-FRA-BLR) & Jet Air (BLR-IXE), the Lufthansa crew did a through check in from LAX to IXE. Hence was easy just to drop the luggage back to to Jetair after pick up from BLR. No issues on luggage weight

Inbound
However, Jet Air (IXE-BLR) had to pay excess baggage fee of 20 kg & Rs 250=Rs 5000.. They don't give any consideration you being a long distance traveler or knowing that you had a though check-in from LAX. However they make/force you eat a worthless sandwich for a 30 min flight from IXE to BLR.

Lessons learnt - Never book a ticket with 2 PNR numbers though its a connection flight provided by the airline.