Hello Daisuke Tanaka!
Could you please create a test build with the tool and open the dev tools, to check if there are any errors regarding the files? Once the test build is ready, run the game and then press F12 to open the dev tools.
At the moment, I can't replicate this. But I have a theory that (assuming that you are on R5) there may be some path handling errors. An update to R6 brought a rework on how relative paths are constructed (so the encryption can work properly, regardless of OS). It is a possibility that the affected files end up on the wrong path (judging from the file not found error in the dev console).