A friend has a factory unlocked 3G. I know for sure it is factory unlocked, because I was the one who upgraded his phone a few months ago to a newer firmware via iTunes and it didn't require activation or any kind of different sim to be inserted. It was on firmware 2.0 and we took it to either 2.1 or 2.2. So for sure it wasn't just firmware upgrade without baseband upgrade.
It was both and the phone was working without the need to jailbreak or unlock.

After some time he wanted to install Cydia and some apps so we jailbrake the phone. Everything was working fine.
Today he decided to upgrade to the latest firmware and he get a locked iphone.
Which is puzzling me. The phone was purchased from a large elecronics store as factory unlocked. It was upgraded and it remained unlocked. And then after another upgrade it gets locked. Any idea guys?

That is strange.

Did you friend have any problems with the iPhone that required it be repaired/replaced under warranty?

Your friend should contact first the company who sold him the iPhone and then Apple. If you have proof that you purchased a factory unlocked iPhone, this should be able to be resolved.

The factory unlock is based on registering the iPhone's unique ID in a database at Apple.

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iPhone 3GS 32GB factory unlocked (3.1; Pwnagetool, Cydia, OpenSSH)
iPhone 8BG (3.1.2; Pwnagetool, Cydia, OpenSSH)