It happens with Debian unstable (evolution 3.12.2-1).

I have evolution installed but no real intention to use it.  I once tried to use with maildir data and pointed it to my ~/Maildir used by mutt.  Then it was messy so I did not use this.

If I click mailto: link and activate evolution, evolution loads my mutt controlled Maildir data and convert it to evolution's maildir++ format without asking me a prompt to stop it.  This quiet conversion is a big problem.

I see this is what happens as evolution started.  If any characters which needs to be escaped from evolution's POV, it change directory name to match evolution's expectation without asking question.
 * It add ..maildir++ file in ~/Maildir
 * If the original directory does not start with ".", it get added.
 * If the original directory starts with ".", it becomes "._2E".
 * If it see's "_", "@", ... , it get changed to "_"+ASCIICODE_IN_HEX

The auto-conversion behind user's approval is very annoying, at least.  If ..maildir++ file is these, this behavior may be understandable (but I would not like it.) 

Please add GUI prompt before invoking such conversion.

Also, I do not see the point of changing my folder from ".Inbox-debian" to "._2EInbox-debian".  If you see Maildir folder having folder name starting with "." and user approve conversion to maildir++ format, use name without leading "." as the sub-folder name.

I also suggest that this maildir to maildir++ conversion feature to offer 2 options for folder name conversion for other part of folder name.

* one to escape as now to show the original folder name in evolution.
* one to convert all these funky characters to "-" (hyphen), so it is easy for other program to be updated to work with this maildir++ format.

Osamu

Thanks for a bug report. This had been fixed within bug #732145, for evolution-data-server 3.12.11.

*** This bug has been marked as a duplicate of bug 732145 ***