I got the same problem.
In my case, I had cancelled, using shell command, one source file from the kinetis project, but kinetis has not updated the makefile structure and looked for the missing C source.
To solve the problem, I've created, using shell command, the deleted file again, then close and reopened KDS, and remove that source file from kinetis.
In this way, kinetis has updated the makefile and now the compilation was success.
Using linux it's easier to use the preferred editor (vi, in my case) and shell commands, with the result that sometime KDS loose the control of the project, but this is acceptable.
Regards. Paolo