I configured NetFlow on Cat6500, but application shows only a few MBytes, whereas it should have been several GBytes.

Cat6500 uses MSFC only for the first packet, and the last packets are switched using PFC (CEF , dCEF ). To correct configure Netflow export on the Cat6500, you must enable Netflow on the MSFC and on the PFC. In your configuration is only the MSFC-netfow enabled, and the majority of traffic (PFC-switched) is missed!
For configuration guidelines see:

http://www.cisco .com/en/US/products/hw/switches/ps708/products_configuration_guide_chapter09186a0080160a2b.html

Or the netflow data from the switch is not getting to the collector anymore.

Check the devices, supervisor and MSFC for config changes.