I sounds to me that you/Revo 'left' the OE mail folders in place with their contents when you 'uninstalled' and some vestigial ancestral memory has awoken to tell you the folders need tidying. I would suggest allowing OE to 'compact', and then forget about it, would be the easiest option. I would hesitate to go as far as 'removing' OE registry entries since as said above, IE and OE are intrinsically bound up as part of the 95/2000/XP OS.
You could have a 'peep' at the OE folders contents if you are curious - Google will guide you. The long-winded 'final solution' would be to put OE back onto your system (reinstall IE), import the 'existing' emails into the 'new' OE, then delete all those emails from OE. That should keep the baby quiet.