Differences in word counts in two files
Change lines like this:

    for word in line1.split(" "):


To lines like:

    for word in (w.strip() for w in line1.split(" ")):


UPDATE:

Here are two ways you could tighten up your function:

1:

    def compute_word_importance(fpath1,fpath2):

        count = collections.Counter()
        with open(fpath1, 'rt', encoding='UTF-8') as fp:
            for line in f:
                count.update([w.strip() for word in line.split()])
        with open(fpath2, 'rt', encoding='UTF-8') as fp:
            for line in fp:
                count.subtract([w.strip() for word in line.split()])

        return len(counter) and counter or none


2:

    def compute_word_importance(fpath1,fpath2):

        def get_words(path):
            words = []
            with open(path, 'rt', encoding='UTF-8') as fp:
                for line1 in f:
                    words.extend([w.strip() for word in line.split()])

        counter = collections.Counter(get_words(fpath1))
        counter.subtract(get_words(fpath2))

        return len(counter) and counter or none