I usually leave "Synchronize Browsing" turned on, as it makes matching the two machines' files much easier. However, if I try to go into a directory one one machine that doesn't exist on the other, WinSCP put up the error message "Cannot open corresponding directory in the opposite panel. Directory browsing synchronisation failed. It has been turned off." I've gotten in trouble a couple of times after this has happened, assuming that "Synchronize Browsing" is on when it has actually been turned off. For example, if after the above error I disconnect and reconnect, I'll be looking at the same directories, but navigating in one will NOT navigate in the other.
Suggestion: if "Synchronize Browsing" is on, and the user tries to navigate to a directory on one machine that doesn't exist on the other, ignore the navigation request and put up the following error: "Cannot change directory because Synchronize Browsing is on and there is no corresponding directory in the opposite panel. If you wish to change to this directory, turn off Synchronize Browsing."
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