Using folders in Mail to keep items on my Mac

Recently I was told by service provider that email account was corrupt and I should delete the account and then add back. I use folders to save email that I need for legal purposes or medical purposes to my mac. When I go to delete email name from Mail it tells me that all email data under that name

will be lost if I delete the account. Will my stuff be safe in folders on my mac or does mail check folders for that email address and delete anything related to it?