MaplePDF Pro pops up a warning dialog if it finds the destination PDF file already exists.
The warning dialog provides three options,
1. Insert the resulting PDF file at beginning of the existing PDF file
2. Append the resulting PDF file to the existing PDF file
3. Overwrite existing file
You can choose the option of your preference when the conflict happens.
To disable this warning dialog for good and all, you would probably be interested in letting the software know your choice in the Output Options tab,
1. Confirm with overwrite options
2. Insert at beginning of existing file
3. Append to existing file
4. Overwrite without asking
Unless you select the first option, MaplePDF Pro will remember your choice each time when destination PDF file is detected to be already in place.