I believe so. To avoid that you would have to exclude also the local directory.
option batch continue
option confirm off
option synchdelete on
option exclude ""
synchronize local -mirror "D:\Backup\home\db\1" "/home/db/1"
synchronize local -mirror "D:\Backup\home\db\2" "/home/db/2"
synchronize local -mirror "D:\Backup\home\db\3" "/home/db/3"
option exclude "/home/db/*/;"
synchronize local -mirror "D:\Backup\home" "/home"
The last action will remove D:\Backup\home\db\1 ?