Thanx, martin for your remark.
I found a funny thing which probably has been known for a while but here is what I found:
clicking on the refresh button in the task menu refreshes the files listed in the GUI window (I'll call them ghost files *). But clicking inside the window, the right click -> refresh makes additional files popping up, that were not shown when clicking the refresh button in the menu bar (I'll call these files X-files **).
After refreshing with right-click inside the window, when I select the * ghost files, WinSCP gives me an error window saying "files not existing!" and then offers me to skip, skip all, cancel, repeat. I choose "skip all", then the * ghost files disappear from the list, leaving only the ** X-files. Seems the X-files are the files that are actually inside the directory, giving the real-time state of the dir content.
So I from now on always and only choose the right-click +refresh inside window method. This way I came a little further and found files that tell me my deployment process is not doing what it should.
This thread can now be closed.