It is possible (although image sequences are usually fine). I suggest you compare your original footage length with the image count (using 25 images per second) to make sure there anr't any dropped frames. One way to check is to import your original footing into vegas into another timeline and u can compare them side by side.

Also, what have you got planned to go into the screens in the UFO interior. I'm in AE atm mucking around with some ideas. Below is a pic still to give you an idea...