We also go by time stamps. If there are multiple plans, we will import the first, at say 10am. We will do all the work needed in AlignRT and in Record and Verify (Mosaiq for us). When it is time to import the second plan, maybe 10:30, then we are then able to tell them apart.
But I agree, it would be WAY better if the file names could be more useful. (And if patient names could be sorted alphabetically in Browse Patient!)