A tool like YATTA might help make things a little easier in some respects. You can do all kinds of stuff with it, but it is a little rough to learn at first.
I suspect it might be helpful in aiding you to quickly identify, and deal with changing telecine patterns.
http://ivtc.org/yatta
Other useful things like the required tools/plugins for using it, as well as some sparse (but still helpful) documentation can be found if you back out to the parent directory.