Hope I'm not too late :)
I've been testing ColdevProLayer,... and it is great. (I hope it is a trustful php extension).
So,... what you can do is, use their phpdesktop just to encode your files.
Then in your phpdesktop, be sure to have thread safe php version and the correct coldevpro php extension version and copy encoded files to your own version of phpdesktop.
For example: your php version (in your phpdesktop) is 7.2. It must be ThreadSafe version. Download from ColdevProLayer github correct version (php7.2.rar)
Take out their extension php_coldevprolayer.dll from ext directory and use/include/enable it in your phpdesktop php.
Now, use coldevpro phpdesktop just to encode all your php files and then copy them to your phpdesktop.
That's it.