Installation - File in Use - Delete?

Hi,
I want to install B & R 11 SBS Advanced and it display a message, that some files are in use. "Backup must delete some files.." "The Program must be closed or the files can be replaced on the next reboot"

One Process is the sqlserver.exe.

Will i get trouble when i install and reboot it?
I have fear to say yes, when the installer will delete files they are part of the sql server..??

Regards