Hi Hannah,
I suspect your check box value is not commited to the database when a user checks it. That would mean the retrieve from database in your microflow will not return the checked objects since the value is only changed in memory.
To solve your issue you need to add a commit action to the checkbox.
ps. if you add an x-path to your retrieve, like “[Selected]”, then the retrieve will be efficient and you won't need the filter action.