Change to Team's Channel "Email Messages" folder naming convention.

I'd definitely contact support first and complain about the change.

However, in the meantime, e-mails come into the folders as eml files, you should be able to just create a flow that triggers on files coming into the library regardless of folder then "Create a copy" into the e-mail folder so it triggers your existing flows, then deletes the file after. Moving might work depending on the trigger of existing flows, but I would look into something like that to just pick them up and move them for you in the meantime.