Getting program to work via IE browers with JAVA Applet

Hi,
I have a C# desktop program being written that the programmers say can't be finished. The program is to login to the users account on IE browser and automatically upload data and images, the problem the programmers say is,

"Well Java Applets can not be automated because they can not be accessed through browser, + the site is SSL secured so we can not automate the backend session as well"

Is this correct? Or is there a way to still make this bot work?

Any suggestions are welcome.

Quan