Would this apply to deskflow also ? If so would you be would to make a patch.

I have changed my layout to "fr" when i type locally i am getting the french keys but when i run the app it still sees English as the layout, and the client will print the "en" layout keys. What method are you using to change the layout ? (this is with deskflow but the code here is basically the same )

Yes, it appears that deskflow needs the same patch. I will create that momentarily.
As for me, I simply have just one non-QWERTY keyboard layout set on my system.
But since the keymap file was not seeked, the read got 0 bytes, causing the LOG_NOTE("Failed to create XKB context: %s", strerror(errno)); to fire, which also left the keymap state uninitialized which ends up defaulting to US keymaps.
To see if this applies to you as well, you can probably check the log and see if you also run into the failure to create the XKB context.