Late answer but might be that can be useful for others. I just get a project with existing watch-kit and custom keyboard code. After change the identifier i got the same error and i spend 1 day to find out why that happens.
I checked everything of bundle id and all version. then i do global search in xcode with old identifier and i found that following.

Here in both .plist file have old WKCompanionAppBundleIdentifier so after i update it with new manually application run again.
IMPORTANT NOTE:
IF YOU ARE JUST CHANGE IDENTIFIER FROM GENERAL TAB THAT DOES NOT MEAN IT UPDATE AT ALL. KINDLY CHECK WITH ALL POSSIBLE PLACES BY SEARCH AND REPLACE IT WITH NEW IDENTIFIER.
XCODE VERSIO: Version 9.0 (9A235)