Stratix IV smd oven reflow cycles allowed

I'm not a process expert but I strongly suspect Altera will only recommend/support a single reflow cycle for their parts.

Altera do have the following application note on the reflow process:

http://www.altera.com/literature/an/an353.pdf (http://www.altera.com/literature/an/an353.pdf)

This discusses 'BGA Rework' but assumes you're replacing a defective device.

It also clearly identifies Altera's process recommendations and identifies the time any device should spend within 5 degreesC of peak - 30 seconds for Pb-Free.

You may argue that providing 2 or more reflows don't add up to more than this period you're fine. However, Altera specify this time as part of a single reflow process. So, unless your process allows this sort of time at peak I'd suggest you're compromising it.