I just came across my own question from years ago when trying to do the same thing again. I'll add an answer here of what I did to help anyone else trying to do the same.
Sugar has a knowledge base article at https://support.sugarcrm.com/Knowledge_Base/Import_Export/Importing_Email_Attributes_and_Multiple_Email_Addresses/ that explains how to import email attributes, such as invalid email. I used it to help me create an import file that would mark the email addresses on my contacts as invalid. I exported a list of all my contacts from Sugar, making sure to include their ID so that when I import them back in it will update the existing record and not make a new one. Used Excel to create a new spreadsheet with just the contacts that had an email address that matched one of the ones from my list of invalid email addresses. Added an "Invalid Email" column with the value set to 1. Then imported that spreadsheet into Sugar to update the existing contacts and set their email address as invalid.