I was using WinSCP 4.0, but I'm unable to recreate the issue in a test setup. I don't want to try it again with my original C:/ backup right now because it would take forever to re-transfer if it did screw up. When I get a chance to troubleshoot, I'll make a new support posting if I run into an issue.

So for now, let's just leave it at "I wish I could have a synchronization list in the GUI without having to write a WinSCP script."

I have tried that myself and it works for me :-( The directories listed in exclude mask are not deleted. What version of WinSCP are you using?

Unfortunately, it doesn't. In this case, I need to make periodic synchs (including deleting files) of everything on a computer except for a few log subdirectories, which should copy new files but not delete the old. The synch script I made does this:
cd /remote/backup/c
option synchdelete on
option exclude "pagefile.sys;logdir1;logdir2;user.dat"
synchronize remote C:/
cd logdir1
option exclude "*.tmp;irrelevantjunk;tmp"
option synchdelete off
synchronize remote C:/logdir1
cd logdir2... etc. etc.

The problem is that the first sync (of C:\) deletes logdir1 and logdir2 on the remote server rather than excluding (which I take to mean ignoring) them. This is also different from the GUI behavior, wherein when I sync C:\ I can just preview and uncheck logdir1, logdir2 and they are left alone on the remote server, easily synchronized later without the delete option.

I hope that scripting would do the job :-)

It'd be nice if for a given host (saved session) one could have a predefined list of directories to synchronize instead of having to do them one-by-one each time.

If you have time (yeah, right) perhaps each directory pair could have its own set of options for direction (remote, local, controlled by direction of parent transfer), overwrite (y/n/ask), etc.

In the meantime, I'll take a look at the scripting options.