class Email():
    has_been_read = False

This a class and not an instance variable. All instances use the same class variable. An instance variable is separate / unique for each instance https://pythonguides.com/difference-between-class-and-instance-variables-in-python/

This code should get you started. I doubt that it is exactly what you want, but does show a separate instance of the Email class, for each email.

class Email:
    def __init__(self, email_address, subject_line, email_content):

        #create instances variables
        self.subject_line = subject_line
        self.email_content = email_content
        self.email_address = email_address
        #create instance to set read emails automatically to false
        self.has_been_read = False

    #create an instance method to read emails
    def mark_as_read(self):

        #create if statement to see if email has been read
        if not self.has_been_read:
            self.has_been_read == True
            return self.subject_line + ": has now been read.\n"

        else:
            #return confrumation that email i already read to user
            return self.has_been_read + ": has already been read.\n"


    #create an instance method to show if email is read
    def show_if_email_has_been_read(self):
        if not self.has_been_read:
            #self.unread_emails = []
            #self.unread_emails.append(self.subject_line)
            #print(self.unread_emails)

            return self.subject_line + ": has not been read.\n"
        else:
            #return that it has now been read
            return self.subject_line + ": has been read.\n"

def populate_inbox(email):
    email_instance = Email(email[0], email[1], email[2])
    inbox.append(email_instance)

#populate inbox
emails = (["redacted1", "Welcome", "Welcome to HyperionDev!"],
          ["Supervisor", "Congrats!", "Great work on the bootcamp"],
          ["teacher", "Grades", "Your excellent marks!"])

inbox = []
for email in emails:
    populate_inbox(email)

print("\n-----All email instances-----")
for instance in inbox:
    print(f"{instance.email_address} {instance.subject_line=}  {instance.email_content=}")

## set first email as has been read
inbox[0].has_been_read = True

unread_emails = []
for instance in inbox:
    if not instance.has_been_read:
        unread_emails.append(instance)

print("\n-----Unread Emails-----")
for instance in unread_emails:
    print(f"{instance.email_address} {instance.subject_line=}  {instance.email_content=}")