After i use WinSCP with with the following line in a .bat file and the source path includes a file with a "." at the beginning, WinSCP running in a issue if the folder in the destination folder doesn't exists (Error Code 3 Permission Denied). That's the minor problem
Please attach a full session log file showing the problem (using the latest version of WinSCP).
To generate the session log file, use
/log=C:\path\to\winscp.log command-line argument. Submit the log with your post as an attachment. Note that passwords and passphrases not stored in the log. You may want to remove other data you consider sensitive though, such as host names, IP addresses, account names or file names (unless they are relevant to the problem). If you do not want to post the log publicly, you can mark the attachment as private.
but the major problem is the Bluescreen after rebooting Windows Server 2019. The Server can't find any Windows installation.
So you mean that after the WinSCP script fails, you restart your Windows Server and it fails to start with a blue screen? Why do you think it is related to WinSCP? On moder versions of Windows, no application running with normal privileges can cause a blue screen.