In those sentences, it's a modal particle, in which case it expresses a change of state. The page you linked has a link to it.
A change of state doesn't necessarily mean an actual physical change. It could be implied, or it could be a change in one's assumptions.
In your example sentences.
Here the change implied is from a state of being in England to a state of not being in England. Yes, it is backwards (!). You have to interpret the sentence from the point of view of the speaker. The first character Ma Dawei is seeing Lin Na after a long time, and he thinks: "I haven't seen her in a long time, she must have gone back to England". But obviously she's not in England anymore, since Ma Dawei is seeing her right now.
So the change implied by Ma Dawei is that Lin Na used to be in England and now she's back to Beijing.
Lin Na then replies:
This change could be relative to two things:
One, it is relative to Ma Dawei's assumption. Lin Na says: "I didn't go back to England, (instead/actually/in fact) I went to Shanghai". Using 了 here stresses the fact that the actual situation isn't what Ma Dawei thought.
Or two, it is relative to the change in location, i.e. she was in Shanghai but she is now back in Beijing. The reasoning is similar to the previous sentence uttered by Ma Dawei.
I interpret Lin Na's sentence as the latter possibility, but one could make a case for both.