cab58 - Welcome to the Board
The most likely cause of your problem is a corrupted Inbox. The maximum size for a folder in OE is 2 GB and OE starts to play funny long before that.
Open OE and create a new Folder - InboxOld and move the contents of the Inbox to the new folder. If OE will not allow this move them to the Spam folder - this is not a native OE folder, but is created by other software. Just be sure that the Spam folder is not emptied automatically when OE is closed.
Then search for *.dbx files - search Hidden files and folders and delete Inbox.dbx - this will be recreated when OE is reopened. Open OE and drag the original mails either from InboxOld or the Spam folder into Inbox. InboxOld can then be deleted. Test. When you have found the .dbx files make a note of their individual sizes - are any over 1 Gb, which I would consider to be far too large for stable operation of OE.
when I tried to go into my deleted message folder, it permanently deleted all of my old deleted messages. Can I recover them?
There may be corruption here too and in this case delete the Deleted Items.dbx as outlined above - with OE closed.
One would assume that if you have deleted a mail you no longer want it - they are not recoverable once the Deleted Items folder has been emptied. If you want to keep a mail it should be stored in a new folder of your own making. OE can be set up to delete the contents of the Deleted Items folder on closing OE - that is the way I have mine setup.