Compaction error since old issue of too little free space........

I continue to have an issue with apple Mail. This started when I had too little hard drive free space. I have now upgraded and added an external hard drive with 2 partitions and have deleted a ton of stuff from my original 8.5gig hard drive to leave me with about 3gigs of free space. I began using Carbon Copy Cloner to back everything up on a weekly basis. Now my issue is that e-mails wont delete and mail will shut down occasionally. It will also give me "compaction errors" and revert the mailbox to original settings. I have tried all of Allan Sampsons suggestions, like going to Applications/Library/ etc. and moving the Inbox to my desktop. etc. etc. etc. ALL has not helped and is just seeming to compound the issue....things keep getting worse. Until just the last few days I was also having shut down issues and "sleep" issues. I ran disk utility and this seems to have been cleared up. I really believe that I have some corruption in my Mail program and would like to remove Mail and reinstall it fresh. Does anybody have any other suggestions? I think I can reinstall with no problem, but I'm unclear how to remove the old corrupted version of Mail. Could someone give me other suggestions or help me through the removal of the corrupted old Mail?

Hello Alana.
Deleting and re-installing the Mail.app rarely resolve this or any problem.
All Mail.app data is stored in the Mail folder at Home > Library > Mail and all email account information and general Mail.app settings are stored in the Mail.app preference file.
Since your hard drive did not have adequate free hard drive space required for OS X to function properly until recently, it sounds like some of your mailboxes (mbox files) have some corruption (not the application itself). If so, re-installing the Mail.app will not resolve this since no data is stored in the application.
Quit Mail first and using the Finder, go to Home > Library > Mail. Move the entire Mail folder to the external hard drive for later use.
Launch Mail and a new Mail folder and account named folders within will be created automatically. All mailboxes will be empty and any created rules and signatures will not be available along with Junk Mail "learned" settings lost but this will determine if the problem lies within the old Mail folder which I believe it does.
If this allows the Mail.app to function properly, you can use the Import Mailboxes function to import selected mailboxes from within the old Mail folder moved to the external hard drive and I would import only a number of available mailboxes at one time since one or a number of the existing mailboxes probably have some corruption due to the lack of free hard drive space you had previously.

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