File layers are not found when you open or command-line export a kra file. This is a bug that was supposed to be fixed by changing the path of the appImage or something (see Boud for more detail, I gave him a kra file with a file layer as a sample at the time). But it's still not working. And also, now everytime you want to save or load a file, the dialog box that shows up doesn't remember the last location you entered but the temp directory in which the appImage is working or so...
It's another aspect of bug 374218 I think. *** This bug has been marked as a duplicate of bug 374218 ***