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.

I'm not sure what you are asking about. You may use two reflow cycles of a board in double side assembly, but FPGAs would be usually placed in the second cycle. In rework, you don't reflow solder a complete board.

Most FPGAs are moisture sensitive devices and must be baked before soldering when exposed longer than 2 to 7 days (depending on the sensitivity level) to ambient air.

Devices can be removed, re-balled and refitted without reflowing the entire board, just applying heat to the particular part. This process cycle would mean a package would be subjected to 3 reflow cycles.

I suspect this is not something Altera recommend or support. They are likely to recommend replacing suspect/damaged parts with new ones.