The OE folder you mention contains all the .dbx files. These are your mail messages. Copy the OE folder to some form of storage media of your choice.
Once windows/OE has been installed again, you need to get the OE folder you copied to be used again by OE.
To restore these messages back into the new OE.
Open OE/ File/ Import/ messages/ select the programme to import from (your version of OE) / select Next/ tick the button marked ‘import mail from an OE store directory’/ click OK/ in the location of messages window, click browse/ now browse to the saved folder you previously created, select OK and they will be imported back into OE.