It is possible. Set the file read-only so WinSCP does not try to write to it.
Version 4.2.7 Build 758
Running on Windows Server 2003
We are running WinSCP from an application server and running some transfers from another server using a .ini file to store the site and application settings. Using the scripting and command line tools to make the transfers we have lost the .ini file a few times and it seems to be when multiple transfers are kicked of concurrently. The .ini file disappears and is replaced by a blank (default) one.
Please let me know what other information you need in regards to the .ini setup or the scripting commands, not sure what specifics are relevant with regards to this issue.
Thanks for your help