Hi Buzy, I am on refeed now but I had the same problem - had loads of days when I only managed two shakes. I have to say I don't think it affected my weight loss but it's hard to tell really.
The two weeks where I skipped a shakes I lost 7.5 then 6.5, then I made a concerted effort to have all 3 everyday and lost 1!
I am not for a second saying that having them all made me only lose 1lb though - I am hoping that was just a blip.
But I was worried like you and when you think of how many calories you are getting by on with 3 shakes, it probably is harmful to just have 2.
Even if it doesn't affect your losses it will affect the nutrients you are getting.
I found a good way to get my third in was to have it as a hot chocolate before bed.
Good luck with it anyway hun x