If I just ignore this prompt, will my script continue to completion and the shell will exit on its own?
Yes it should.
If the answer to number 1 is No, how to I prevent this prompt from showing? When I set Batch Mode On the script auto exits on the first prompt which is bad..
You can set longer timeout on login dialog.
I set a 999 timeout on the login dialog. But that doesn't actually save it does it? I have to save the 999 timeout to a specific session it seems like.
When I run the batch script to connect to a server, it still says timeout after 15 seconds. How can I set the default timeout to be higher so that the command line batch script for winscp can have a long timeout as well?