The keybinder config file is in the %APPDATA%\codeblocks or ~/.config/codeblocks directory (windows or linux/mac). The file you are after is <personality>.cbKeybinder20.conf where for normal users <personality> is default.
Can you make the customized Keyboard Shortcuts changes and then make a copy of the <personality>.cbKeybinder20.conf file in the same directory and then update to another nightly and if the shortcuts have been removed can you raise a SF Codeblocks ticket (see
https://forums.codeblocks.org/index.php/topic,1427.0.html for info) and include the two config files along with with some of the custom keys you have added so that when someone looks at the bug ticket they can reproduce the bug and check out the config files.
Unfortunately I don't have any time to investigate the issue until the end of next week.
