I would like to give some information on this topic, since the thread doesn't contain a solution. I don't know if Qtip5 has been able to solve this problem or not.
An AM user contacted me with this same problem:
When she tried to compile a project, she got the message "Error compiling the project. File already exists."
After looking into it, we could solve the problem.
There have been game files in the Temp folder of AM, and this has prevented the compilation process.
When moving the content out of the Temp folder (in a first step just to the My Documents folder on the harddisk to be able to move it / or some parts of it back if necessary), the project could be compiled successfully