This problem used to happen in previous versions of Windows and users had found workarounds for it (http://answers.microsoft.com/en-us/windows/forum/windows_8-desktop/custom-hotkeys-to-change-input-language-disappear/66d1d89d-e5dc-41e1-a8b3-48d596ab8e11). However those soloutions do not work for Windows 10.
I have 3 keyboards and I have defined Ctrl+1, Ctrl+2 and Ctrl+3 hotkeys for them. The problem is that either all of the hotkeys or the first one is removed regularly (when windows goes to sleep or lock screen all the hot-keys are removed).
This makes me crazy when I am in hurry to get something done (and the problem kicks in).
Please do not suggest blind generic (mostly nonsense) solutions like running sfc etc. I have done most of them without luck.