If these members have been home for more than two years then it's possible that some of the data has already been deleted from MLS due to the "retention period" having passed for that time. Also, the transition to CUBS likely happened while they were serving as full-time missionaries and, if your ward's records were affected the way our ward's records were affected, it is almost impossible to reconstruct some of the missionary donation data pre-CUBS. (Certain data was impossible to recover at the moment the CUBS transition took place, not to mention the years that have passed since then.) If you didn't print out certain reports before the CUBS transition you were in trouble trying to sort things out after the transition.
So what I'm really saying is you might just have to examine any excess funds in the Ward Missionary Account that aren't earmarked for any given missionary and use them to zero out these sub-categories for returned missionaries. Any attempt to investigate such old details and find out the real history is probably futile. (And I hope you didn't recently give a whole bunch of excess funds to the stake or to CHQ thinking it was excess but it was really needed to clear up this problem.)
My real name is Greg Anderson.