What I believe is happening is that when rescan reads the card it flips a bit or switch that causes this, If you allow the S9 to overwrite the card nothing appears to happen nor do you appear to lose any data as the next time you use it with rescan it asks if you want to overwrite duplicate data or ignore it.
I think the S9 has some onboard temporary memory so you lose nothing.
However I have found a way to not get that message at all.
When you remove the sd card from the S9 lock it with the tab, Rescan can still "read" it then before reinserting back in the S9 unlock it. No message except reading card,