it works!
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Bug reports without an attached log file are usually useless.
@echo OFF
cd winscp
winscp3 /console /script=scpcomd.txt
echo.
echo.
echo Update completed.
echo.
echo Dear user,
pause
option batch on
option confirm off
option transfer automatic
option synchdelete on
open user:pass@my.server.com:22
synchronize remote .\..\Web /home
close
exit
synchronize remote .\..\Web /home
then parses the winscp.ini file in order to change the entries with the appropriate drive letter
The only entries that I see in the ini file that are drive letter dependent are RandomSeedFile, Puttypath, and PublicKeyFile.