I haven't used this tool either, but have heard that it never converts all the old tag names for you.
The "e's" are indeed indicating an undefined tag. Look for the tags in the rung with the "?"s underneath. You can quickly create these by right-clicking on the undefined tag and selecting "create new". From here you can define the tag type, size (if an array), and scope. Most of the time the type will default to the correct type for the instruction its placed in (Timer for TON, Bool for an OTE, DINT for a MOV destination etc)