The solution behind this problem is to install Flexget as a normal user, since when upgrading it shouldn't be able to touch any important binary.
As a prerequisite you need pip (at least the one for python2.7) and setup-tools installed as root. Once the prerequisites are met, you can install Flexget with the following:
pip2 install --user flexget
That will download, build and install all the needed components under the .local folder inside your user's home directory. The Flexget binary will be in $HOME/.local/bin
If you have Flexget already installed as root, you would need to uninstall it first, check that the prerequisites are met and then change to the user you want to install from and run the above command.
The update command when Flexget is installed as a normal user is the same as it would be as root but adding the --user flag:
pip2 install --upgrade --user flexget