To me that makes sense; but I would expect that if you manually triggered File > Update Indexed Items the problem should be solved. I guess, but don’t know, that at that point the “original” record would be removed from DT (as it is “missing”) and a “new” record would be created. The disadvantage is that any metadata you had added to the record in DT (tags etc.) would be lost.
Out of interest: do you keep DT open at all times? I kind of thought it would notice any changes made to an indexed folder whilst it was alive and kicking and that only changes made whilst it was in bed asleep would be a problem. But I don’t have any basis other than assumption for that claim.
I think this thread answers your question.