M-x set-buffer-file-coding-system and select the desired coding system.
This is, by default, bound to C-x RET f.
Notice that C-x RET is a prefix map. For more info, C-x RET C-h (or equivalently C-x C-m C-h).
You can try to find out what triggers it by doing M-x debug-on-entry select-safe-coding-system (then read until the debugger gets triggered).
For me the pop-up seems to get triggered by git-gutter-mode. Simply deactivating that mode stops the very annoying behavior.
(Subsequently, the debugger also got triggered by pdf-view-restore, but the problem was ...