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As to the Pop3 files, you can leave them behind or delete them at any time and OE will create new ones the next time you download e-mails. But, if there are still stacks of e-mails on the Server(s) that you already have, being held there for the time you specified on the Advanced Tab in the User Account(s) Properties, you will just get duplicates. Eventually they disappear from the Server(s), of course. Taking the Pop3 log files with you just avoids all those duplicates.
Those old .dbx files are just detritus. When you deleted the folders in OE the files were left in the Identity Folder. You can let them go. But try doing it by using the File/Folder/Compact All Folders command. That'll also get rid of the stuff within the wanted folders that has been deleted. You may notice that the Deleted Items File is quite big even though you have just emptied it.
Finally, this is a good stage to change the names of OE Folders if you want by renaming the corresponding file and making sure you create a folder in OE with exactly the same name.