Gmail.com has the same messages in its inbox and a number of other mailboxes, o.a. Important. When deleting messages from the inbox and refreshing the mailbox Important (by pressing F5), these messages are also gone from the mailbox Important in an earlier version of KMail. However in KMail 3.13.80 this is no longer the case.
The same problem in KMail 4.14.0 to which I updated today.
Problem gone in 4.14.1