Anna,
If your lo is really showing no interest in the 11am bottle, I would try and decrease the amounts of solids at breakfast a bit and see if this makes any difference.
It is not uncommon for a lo at 6 months to drop down to 3 bottles a day, you just need to ensure that you have tried all the options. Our DS did this at 6 months.
Are you on a fast flow teat? Is this the only bottle that he is not showing interest in? Could he be teething?