An update: I've now repaired about 50 emails from various senders, over a few days. Most messages have 2 occurrences of "base64" and a few have just 1 occurrence. Replacing the 2d or only one with "quoted-printable" always has worked. A few oddities:
- TextEdit on earlier versions of OS X often finds fewer occurrences of "base64" and often finds no occurrences. We didn't troubleshoot that to death; we could have been executing the search incorrectly (unlikely). Best to stick with TextEdit under Yosemite, or another text editor of your preference.
- there may be no way to search for corrupted emails; in Mail.app, using the black diamond stood on end with the question mark in the middle, we usually turn up a few results, mostly just from odd characters around signatures, but miss most of the truly corrupted emails
- search results on senders of emails where attachments have been removed are bizarre: the email in the Trash folder shows as a result, with the attachment still attached; the near-duplicate email (i.e., the one without the attachment, outside the Trash folder) does NOT appear in the search results
- occasionally, moving an email off iCloud (and maybe other IMAP mail servers) to another folder "On My Mac" generates 2 .emlx files -- we didn't test this extensively, and the workflow may have involved the removal of attachments while the email was in the "On My Mac" folder. We also were able to produce a 3d .emlx file while working with the same one email message. When this happened, we used TextEdit to make the base64 revisions to each .emlx file. Back in Mail.app, even after the message was fixed and moved back onto iCloud, the 2 or 3 .emlx files remained in the "On My Mac" folder. They disappeared once Mail.app was quit and re-launched.
- on one occasion where we think the wrong (1st of 2) base64 occurrence was changed, we lost the entire text of the email and couldn't figure out how to make it reappear (moral: until you're comfortable doing this "under the hood" stuff, you may want to duplicate the .emlx files you're fixing, so that if you experience text loss or other weirdness, you can revert to the copy)
- using a short-cut for "quoted-printable" through TextExpander makes this process MUCH simpler; there's probably a better way to automate this tedious process, but I'll leave it to you coder types to show us that way
HTH,
Ted