I have a file that sends one type of email to one group of people and I have another that sends another type of email to another group of people. Both files call the same phpmailer folder.
If they are called at the same time, is there a problem with sending the email?
No problem. You can have as many different scripts as you like using the same PHPMailer library at the same time. So long as you keep your scripts that use PHPMailer separate, there are no problems doing this.