Nope. It carried on for four more seasons after FTF.
I don't really know how they got back, but apparently the writers were aware of the plot hole as well, because Mulder made a joke about it at some point during the sixth season. I think they just acknowledged it was a plot hole, and left it at that without ever trying to explain it because the first episode of the next season barely even touched on any of the stuff that happened in the film other than the X-Files being reopened.
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