According to earlier articles about this issue, planes currently in wide use need to be 'rebooted' at a similar frequency, it's just specific subsystems that get rebooted (I think the F-35's former problem was a sensor), the planes keep flying, and missions don't often last that long anyway (IIRC all the details).
Here, I found the link:
https://news.ycombinator.com/item?id=11260927
EDIT: Heck, I'll just copy the meat of it here:
http://breakingdefense.com/2016/02/bogdan-predicts-f-35s-for...
The toughest problem the program is having is matching the timing of the aircraft’s fusion software with its sensors’ software. “As we add different radar modes and as we add different and capabilities to the DAS system and to the EOTS system, the timing is misaligned,” and then you have to reboot it. Bogdan said he’s aiming for eight to nine hours between such software failures when a radar or DAS or EOTS needs to be rebooted, which is what legacy aircraft boast. Right now they are at four to five hours between such events. “That’s not a good metric.”