One of my earlier posts covered routing Netflow Exports to a server over IPSEC. The previous covered method relied on the use of GRE tunnels and loopback interfaces to forward the export to a central router which in-turn then forwarded them onto the collector.
The question of why bother and just not use a Cisco ASA to terminate the VPN could be raised and I guess the requirements and the methods of the outgoing connectivity will have input. However, the ASA will support the exporting of Netflow over and IPSEC tunnel and adding no funky workarounds. The two key things to remember are:
Add the collector to your INSIDE interface
Ensure the collector is covered by Interesting traff