As the title reads this happens if you use another command.com interpreter which would require the VERSION CONFIG.SYS internal command to be loaded.
A solution would be to also transfer CONFIG.SYS.
However, if the custom command interpreter is not exactly named "COMMAND.COM" it will fail too. So a more complex solution would involve scanning CONFIG.SYS contents to see the actual filename of the SHELL, and transfer that one instead of COMMAND.COM. Of course, the CONFIG.SYS file will also be needed to be transferred with this approach too.
Tested on the bleeding edge 2025 build.