Guneet,
If I had to guess, your .TBN files were 0K because all of your routers were stuck in RebootRefresh status. This can happen if there is a problem with the Harvesters doing SNMP polls of your routers. See the following doc:
Why does my NFA stop displaying data for a router if it cannot be SNMP polled?
Note: We do NOT recommend turning on IgnoreReboots, I'm just sending this doc to help explain what you are seeing.
As for why a rebooting fixed the problem, I suspect that the root cause of the problem was that the "CA NFA Collection and Poller Webservices" service was hung. Restarting these two service and then repolling your routers from the GUI would probably have had the same effect:
CA NFA Poller
CA NFA Collection and Poller Webservices
Check the following log file on the Harvester from the time period before the reboot:
CA\NFA\Netflow\Logs\collpollws-wrapper.log