+ AA6YQ comments below
I was reconciling DXCC verified credits this week and saw the same behavior. When I filtered the log on a DXCC country prefix, if the selected QSO in the filtered list had 00:00:00 as the begin time, the "Changed item in QSO already uploaded to LoTW" appeared immediately. It also appeared every time I selected that QSO again, i.e. when I pushed the |< or >| buttons to move to the top or bottom of the list. DXKeeper v15.9.9.
+ Thanks, Mike. Until I track down and correct the responsible defect, you can uncheck the "Prompt on change to logged QSO already uploaded to eQSL.cc and/or LoTW" option on the "QSL Configuration window's General tab.