Hi Bob,
are you using an IMAP or a POP account with eM Client? If you’re using a local data account, my best suggestion would be removing your account from eM Client and import all your data (including folders again).
Using the Import from Thunderbird should allow you to select which folders will be imported into eM Client, check if these are visible and make sure to deselect them before importing. Unfortunately there’s no option to delete multiple folders at once using the current setup.
Thank you,
Paul