The idea is to iterate through the items and verify the conditions:
from PyQt4 import QtCore, QtGui
import random
class Widget(QtGui.QWidget):
    def __init__(self):
        super(Widget, self).__init__()
        self.tree = QtGui.QTreeWidget(columnCount=3)
        self.tree.setHeaderLabels(["column {}".format(i) for i in range(3)])
        button = QtGui.QPushButton("Press Me", 
            clicked=self.on_clicked)
        lay = QtGui.QVBoxLayout(self)
        lay.addWidget(self.tree)
        lay.addWidget(button)
        self.create_data()
        self.resize(640, 480)
    def create_data(self):
        for i in range(4):
            it = QtGui.QTreeWidgetItem(["file{}".format(i)])
            self.tree.addTopLevelItem(it)
            for j in range(random.randint(2, 5)):
                vals = ["+", "found item-{}-{}".format(i, j), "new item-{}-{}".format(i, j)]
                child_it = QtGui.QTreeWidgetItem(vals)
                child_it.setCheckState(2, random.choice([QtCore.Qt.Checked, QtCore.Qt.Unchecked]))
                it.addChild(child_it)
        self.tree.expandAll()
    @QtCore.pyqtSlot()
    def on_clicked(self):
        d = dict()
        for i in range(self.tree.topLevelItemCount()):
            top_item = self.tree.topLevelItem(i)
            v = []
            for j in range(top_item.childCount()):
                child_item = top_item.child(j)
                if child_item.checkState(2) == QtCore.Qt.Checked:
                    v.append(tuple(child_item.text(i) for i in (1, 2)))
            d[top_item.text(0)] = v
        print(d)
if __name__ == '__main__':
    import sys
    app = QtGui.QApplication(sys.argv)
    w = Widget()
    w.show()
    sys.exit(app.exec_())
Output:

{'file0': [('found item-0-2', 'new item-0-2'), ('found item-0-3', 'new item-0-3')], 'file1': [('found item-1-0', 'new item-1-0'), ('found item-1-1', 'new item-1-1'), ('found item-1-2', 'new item-1-2')], 'file2': [('found item-2-0', 'new item-2-0'), ('found item-2-1', 'new item-2-1'), ('found item-2-3', 'new item-2-3')], 'file3': [('found item-3-0', 'new item-3-0'), ('found item-3-1', 'new item-3-1')]}