We just did this (I posted about it on another thread). I had a bit of a hard time with it - one CM felt one way and one thought we should still get it. Here's what I wrote:
We had something similar to this happen - not the Character breakfast entrance, but we did a split stay (first on site and then on Harbor). On the Tuesday when I qualified for EMH due to staying onsite, I asked the CM at the turnstile to ensure that I was being let in on my hotel entry and not using up the MM (so I could use it Thursday when we would be staying offsite). The CM beside her said that wasn't allowed. The CM I was dealing with thought I should be and told me I should bring my room keys Thursday to explain (which I wasn't too pleased about, but we were the first in line with a crowd behind us so I thought I would just go to Guest Services and sort it our later). But then when I went to get a FP it revealed that the tickets weren't scanned properly, so I am wondering if that's how the CM let us in without screwing up the MM (i.e., somehow did that purposely so I wouldn't have trouble on Thursday, although I have nothing to back this up...).
It did make me very wary of doing anything like that again, though....