Isn't it the other background instance that pops the notification?
Aren't you downloading in the active instance (and that triggers re-upload of the newly downloaded file in the background instance)?

Hello, I have 2 instances open to the same server. One instance is in background for synchronize and one is open and working with.

If I now copy a file in the active WinSCP and it is finished, a Windows notification now appears that the queue is empty. Normally you only get this when the application is in the background. But here I am directly in it and it is active. I assume that because a second connection (in background) to the same server exists?

Since I have the window open and am actively working with it, I do not need a Windows notification for this instance. For the other instance in the background, there should of course be a notification.

I hope that has been understood somehow :)