PKHEX showing Pokemon in box slots that are empty in-game

[Echo7Solo]

I'm pretty new to PKHEX and haven't been able to find an answer to this, and I apologize if this has been answered elsewhere already.

Basically, PKHEX is showing Pokémon that have since been removed from their former slots and placed in my Poke Bank account.  Is there a way to fix this?

Thank you in advance for the help.

Edited May 10, 2018 by Echo7Solo

[Kaphotics]

You aren't loading the latest save file if they still are appearing. Dump your save file again.

[Echo7Solo]

That did it. Thank you! ...Did I mention I'm new to this?