k, think i know whats happening here. look into it more tomorrow.
but there's code that says check if the working file is changing and if its not the original file, delete the current working file.
so since you did a rename, the working file changed, then once the conversion happens, that is now set to the working file, and the renamed one isn't the same as the original file, so it gets deleted.
I just have to put in a check to only delete from the temporary directory.
I'll confirm this tomorrow and fix it in RC2, just waiting for any more bug reports to come in.