There are both in Netflow v9: according to rfc3954:
- section 5.1: sysUptime is the Time in milliseconds since this device was first booted.
- section 8: LAST_SWITCHED and FIRST_SWITCHED sysuptime in msec in which respectively the last/first packet of this flow has been switched.
So you can have both a sysuptime for a flow or the whole device. Looks like your original question is about the header of a Netflow packet, so that would be the uptime of the device.
One last thing: the sysUptime value can only record about 49 days, since it is a 32bit value.