Pleased with the Betas of El Capitan. But Mail seems to crash, consistently, with all of them so far. I've rebuilt Mailboxes. Not sure what more to do. Just random crashing, responding from incorrect e-mail accounts, missing e-mail accounts in drop down menu. All of this, sporadically.
Look in the User's Library/Mail folder. El Capitan Mail is stored in V3 folder. One of the changes is the accounts are no longer in the folder names but Mail now names all mailbox folders like this:
9BE2DCEA-42E2-4520-81B1-5FB4C43E652D
58C52118-7830-4962-BF48-DD672B225083
730D4234-5228-41E8-839A-310FC2A69004
9082A243-BAC9-4C69-8D46-58005F095A34
047978CF-D663-4EC9-8F5E-843582C0C9C4
C7AA1753-CDA7-4C5D-9505-05B73B565A50
C9A984AA-A145-4988-8279-B93445951DAB
I found that some of my account had upgraded to the new naming scheme, but others had not. Even the Mailboxes folder for the local "On My Mac" folders have the same numbering for name.
If you are seeing similar, I would delete all accounts in System Preferences > Internet accounts (you also might want to start with a clean V3 folder. Mail Data is the only folder you'll want to keep) and let Mail download all your accounts from the server again.
All this is assuming you have no POP accounts. If you do have POP be sure you export all your local Mailboxes especially the Inbox.