You often get little understanding from work colleagues. How could they possibly understand it if they've never had it.

To start with I had a lot of time off, but once I was diagnosed properly and got the right meds it was all fairly easy. I had sumatriptan auto injections. As soon as I felt a CH starting, I would make a quick trip to the ladies room with my injection and most of the time no one knew.

I work in an office and sometimes when in the bathroom dealing with Cluster can be away from my desk from 15 minutes to over an hour.

Bob gives good advice.
Pressures from work add more stress to your situation and anything you can do to alleviate this will be a great help. You have enough to deal with as it is.
Along with the letter (if you use it) try to show that you are doing everything to resolve the CH and that you won't allow your life to be controlled by this thing. My experience is that some colleagues, once they understand that, actually start to support you.
Good luck,
Peter.