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.