The Sony recorder will record whatever source you've set it to, either it's own analogue tuner, it's Freeview tuner or one of the line inputs. If you have your Freesat box plugged into Line 1 for example and have set the recorder to record that line, it'll carry on regardless of what you tune your tv to. The only time you'd have a problem is if you're watching TV via the feed from the recorder, but that's only necessary if you're viewing a recording.
In this part of the country we don't have Freeview, which is the main reason for me getting Freesat, so I can't give you an answer from experience of Freeview, but I don't see how you would have a problem.
My TV has it's own Freeview tuner built in, so in your situation I'd just switch to the TV Freeview tuner. That wouldn't affect the recorder or the Freesat box.
Hope I'm making sense.