Maybe automatic selection of transfer setting preset may help you. Please check a documentation.
I am using WinSCP for two main purposes
1. Backing up my windows source code onto a linux server.
2. Maintaining linux based websites.
For the first one, I want to make all of the target files lowercase so that duplicates do not occur when copied back to Windows.
For the second one, I want to retain the case of filenames - otherwise the linux based websites will eventually run into trouble with existing/updated files.
It would, therefore, be really handy to be able to have this option attributed to particular sessions rather than being a global setting.
Would this be possible? If not then I will have to remain with my current ftp client (yuk) for updating the websites.